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file mode 100755 index 00000000..627da9c6 --- /dev/null +++ b/web/tutorial/WebQTLTour/index.html @@ -0,0 +1,294 @@ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> +<HTML><HEAD><TITLE>An HTML Guide to GeneNetwork and WebQTL</TITLE> +<META http-equiv=Content-Type content="text/html; charset=iso-8859-1"> +<base href="http://www.genenetwork.org/"> +<LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'> +<LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'> +<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT> +<SCRIPT SRC="/javascript/tooltip.js"></SCRIPT> +</HEAD> +<BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff> +<TABLE cellSpacing=5 cellPadding=4 width="100%" border=0> + <TBODY> + <!-- TOP BANNER --> + <TR> + <script language="JavaScript" src="/javascript/header.js"></script> + </TR> + <TR> + <TD bgColor=#eeeeee class="solidBorder"> + <Table width= "100%" cellSpacing=0 cellPadding=5> + <TR> + + + +<div class=Section1> + <h1><span style='font-size:18.0pt;font-family:Verdana'> GeneNetwork: A tour and tutorial <A HREF="/webqtl/WebQTL.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0></A></P> +</span></h1> + +<DIR> + +<DIR><I><SMALL>This text is taken from the GeneNetwork Tour available at http://www.genenetwork.org/tutorial/WebQTLTour/ . See GeneNetwork Help menu for find the latest version of the Tour.]</SMALL></I></DIR> + +<p><b>Aim of this tutorial. </b><span style='font-weight:normal'> +The goal is to illustrate how to use GeneNetwork (GN) to study gene function and relations between genes and traits such as differences in disease severity, differences in anatomy, and differences in physiology and behavior. You can also use GN to study relations among phenotypes, for example: to what degree does an injection with cocaine or alcohol lead to an increase in movements? Most of the experimental data sets in GN are from small populations of mice (e.g., the BXD family of strains) and rats (HXB family). There are also some human, monkey, drosophila, and plant data sets to explore, although you may find that mapping functions have not yet been implemented for these other species. + +<P>The focus in this tutorial is how to use some of the most important functions. You should be able to complete this tutorial in about an hour. For this demonstration we will study expression of a key gene known as NR2B or <I>Grin2b</I>. This gene/mRNA/protein is crucial in learning and memory. Once you have worked through this example, you should be able to use GN to explore single genes or set of genes, mRNAs, and other standard traits that interest you.</span></p> + +<p><b>What you will learn. </b><span style='font-weight:normal'> If you spend an hour working through this tutorial you will learn how to extract dozen of molecules that potentially interact with NR2B. It will be easy for you to generalize what you learn to any other gene or transcript of interest. You should be able to confirm known relations (information from the literature) and you should be able to uncover intriguing new relations among sets of molecules and other traits. You will learn how to exploit a gene ontology (a gene ontology is a simple and systematic way of categorizing the functions of genes) and you will also learn about gene or QTL mapping and complex trait analysis.</span></p> + +<P>By the way: if a term is new to you (What is a <A HREF="http://www.genenetwork.org/glossary.html#Q" class="fs14" target="_empty">QTL</A>?), and you would like to read an explanation then have a look at the GeneNetwork <A HREF="http://www.genenetwork.org/glossary.html" class="fs14" target="_empty">Glossary</A>. + +<P>Much of the data in GN were gotten from gene array experiments. As you have undoubtedly heard or experienced yourself, the analysis of array data sets is difficult and sometimes messy. You may encounter poor quality data in some of these enormous data sets. An important part of learning how to use GN involves tools to evaluate data quality. Treat the results you generate with GN with caution. There are solutions to some problems you run into, but for other problems, including comparison across multiple data sets. + +<P>After you have worked through with this tour, please look quickly at the <A HREF="http://www.genenetwork.org/faq.html">Frequently Asked Questions</A> and the <A HREF="http://www.genenetwork.org/glossary.html">Glossary</A>. Let me know if you have other questions or if you see mistakes that I should fix. Email should go to Rob Williams (rwilliams@uthsc.edu). + +<p><b>Step 1: Getting the terminology right.</b> +<span style='font-weight:normal'> + +The use of gene symbols and names in research papers is not consistent. When you search databases it helps to use the preferred or official gene name and symbol. In most papers, the NMDA 2B receptor is abbreviated <I>NR2B</I> and a Google search for "NR2B" will generate about 100,000 hits, many of which deal with the genetics and molecular biology of learning and memory. But it turns out that <I>NR2B</I> is not the official name of either the gene or protein. A great way to verify nomenclature is to go to </span><A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene"_blank"> NCBI Entrez Gene</a><span style='font-weight:normal'> and enter the gene name or symbol. Entrez gene should be able to resolve your query and give you the correct symbol. </span></p> + + +</Dir> +<p> +<img width=735 height=500 src="/images/upload/Tour_1_NR2B.png" v:shapes="_x0000_i1025"></p> + +<DIR> +<p><B>Figure 1: Getting the terminology right</B> + +<p>When we enter <b>NR2B</b> or <B>nr2b</B> <span style='font-weight:normal'> we find that the official gene symbol in Entrez Gene is <i>Grin2b</i></span> for mice. The corresponding human gene is the same, but written entirely in capital letters <I>GRIN2B</I>. In both species the official gene name is <i>glutamate receptor, ionotropic, N-methyl D-aspartate 2B</i><span style='font-style:normal'>. </span></p> + +<p><b>Step 2. Linking to the GeneNetwork search page</b><span style='font-weight:normal'> + +Link to GN at </span><B>www.genenetwork.org/</B>. Ideally, keep this tutorial page open at the same time so that you can look back and forth between the two windows.</b><span style='font-weight:normal'> You have a few choices to make: Choose species = <B>Mouse</B>, Group = <B>BXD</B>, Type = <B>Hippocampus mRNA</B>. We have a great deal of data for the BXDs, so when in doubt, please select the BXD group of mice. Having made these choices, you still need to pick a particular database; in this case an array data set for a particular brain region called the hippocampus that, like NR2B, is critical in learning and memory. For the purpose of this tutorial, choose the database file called: + +<P><B>Hippocampus Consortium M430v2 BXD (Jun06) PDNN</B> + +<P>You can set your particular choice of species, group, type, and database as your personal default setting. Simply click on the <B>Set to Default</B> button (lower right). If you want to know what this long database term is all about, click on the <A HREF="http://www.genenetwork.org/dbdoc/HC_M2_0606_P.html"<B>INFO</B></A> button immediately to the right of the database name. + +<P>Now enter your search terms in either of the search term fields labeled <B>Get Any</B> or <B>Combined</B>. <B>Get Any</B> is usually best and will search for all of the entries you put in this field (logical OR). <B>Combined</B> will only get records that match all of the terms that you enter (logical AND). You could enter both </span><b>NR2B</b><span style='font-weight:normal'> and </span><b>Grin2b</b><span style='font-weight: normal'> in the </span><b>ANY</b><span style='font-weight:normal'> field. You can also use wildcard characters ? and * for single or multiple characters. It is often a good idea to enter an asterisk after a search term, such as Grin*. This will get all subunits of a molecule or complex. + +<p ><a name="OLE_LINK1"></a><a +name="OLE_LINK2"> <img width=716 height=677 +src="/images/upload/Tour_2.png" v:shapes="_x0000_i1026"> </a></p> +<p><B>Figure 2: The Search Screen. This is the page to bookmark.</B> + + +<p><b>Step 3. Retrieving the data.</b><span +style='font-weight:normal'> When you click on the </span><b>Search</b><span style='font-weight:normal'> button, your computer sends this string of search terms to GN (GN is an Apache-Python-MySQL web database system), which then looks through thousands of records for matching terms. The database that we just searched has 45,101 entries that represent close to 20,000 known genes and expressed sequence tags (ESTs). (To determine the size of any database enter a single asterisk (*) in the ANY field.) +</span></p> + +<p><span style='font-weight:normal'> <img width=822 height=688 src="/images/upload/Tour_3.png" v:shapes="_x0000_i1027"> </span></p> +<p><B>Figure 3: Search results for the search string <I>Grin2b</I></B> + + +<p>In this particular case, if you entered just "Grin2b", your will get at a list of six data sets. The last three are measurements of <i>Grin2b</i></span> expression. These thee measure different parts of the mRNA: the distal 3 prime UnTranslated Region (3' UTR), the 3' region of the last coding exons (coding exon 12), and an alternative 3' UTR of a short mRNA splice variant (an mRNA isoform). Which of the three should you pick? The best choice is usually the that which corresponds to coding sequence. In this case, you should study the 5th entry highlighted in red. You an come back to the other two data sets later to see how they compare. And you can ignore the top three <I>Kif17</I> data sets that were found only because the gene description includes the text "NR2B/GRIN2B NMDA receptor transporter." + +<p> <img width=703 height=29 +src="/images/upload/tutorial_banner.jpg" v:shapes="_x0000_i1028"> </p> + +<P>This is a good point to review several of the features most GN pages. Feature 1 is the banner of terms toward the top labeled <b>Home, Search, Help, News, etc.</b><span style='font-weight:normal'> etc. Most of these menu headings have pop-down lists from which you can select additional resources and tools. For example, the </span><b>Search</b><span style='font-weight:normal'> menu heading lists the <B>Search Databases</B> page (our starting point), the <B>SNP Browser</B> tool, the <B>GeneWiki</B> resource, <B>Interval Analyst</B>, and <B>GenomeGraph</B></span> displays. These features are worth trying out later. The <b>Policy</b><span style='font-weight:normal'> menu explains how to contact the data providers and how to use and cite data. </span></p> + +<p>Another useful feature of the Search Results window is the <B>Sort By</B> selector. You can sort longer lists of "hits" by their location, their expression levels, or by their maximum LRS or LOD scores. There are also small check boxes to the left of each entry. These are used to select data you would like to move into a Collection. The <b>Add</b><span style='font-weight:normal'> button will move any checked items into your collection. Collections can include any gene, trait, or SNP marker that has measured in the BXD family. You can even add your own BXD data using <B>Enter Trait Data</B> in the MAIN menu (top left). The ability to add diverse data types into a Collection provides a great deal of power. The use of the <B>Collections</B> is a topic for a more advanced tour. Let's get through this quick tour and then feel free to build up your own collections of phenotypes for "collective" analysis. + +<p><b>Step 4. Reviewing the NR2B expression data.</b><span style='font-weight:normal'> +Roll you cursor over the term </span><b>ProbeSet/1422223_at </b><span style='font-weight:normal'>in the</span><b> Search Results</b><span style='font-weight:normal'> window. This is the probe set that targets the last exon of the <I>Grin2b</I> transcript. The text will turn red. Click on the term. This will generate a new page called the Trait Data and Analysis Form. + +This </span><b>Trait Data and Analysis Form</b><span style='font-weight:normal'> page is the most important page for the analysis of genes and traits. We will return here several times. The top of this page contains useful background information, including the database that we used, the trait identifier, gene symbol and aliases, the chromosomal location and megabase position (Mb) of <i>Grin2b</i></span> in the mouse genome. GN also includes links to NCBI, OMIM, GenBank, BioGPS, STRING, PANTHER, Gemma, and the Allen Brain Atlas (ABA). To find out more about these resource, just click on the links. There are also many additional useful links under the <A HREF="http://www.genenetwork.org/links.html">Links</A> menu heading.</p> + +<p> <img width=765 height=494 +src="/images/upload/Tour_4.png" v:shapes="_x0000_i1030"> </p> +<p><B>Figure 4: Trait Data and Analysis Form for <I>Grin2b</I>, probe set 1422223_at</B> + +<P>Eight buttons shown in Figure 4 and you need to know what most of them do. +<OL> + +<LI>SNP Variant Browser: This link provides you with a list of all known SNPs in <I>Grin2b</I> that are in the GN database. You can, of course, also search for SNPs in other genes or regions. The SNP Variant database is pretty well populated (about 8 million SNPs) and includes all of the Celera SNPs and many SNPs from Perlegen, NIEHS, and our own in-house sequencing projects. As of Jan 2011, there are nearly 7000 SNPs in <I>Grin2b</I>, but only about 20 of these are in exons. Click on the SNP Browser button to have a quick look 9you may need to restrict the SNP search to just <B>Domain = Exon</B>. + +<LI>GeneWiki: This link lets you annotated our databases. You can leave yourself notes and comments about particular genes or probe sets. You can easily find your own notes using a special search string described in the <A HREF="http://www.genenetwork.org/searchHelp.html">Advanced Search</A> page. But in short your search would be written out "wiki=myName". Leave out the quotes and make sure that "myName" is in your Wiki entry. It is that simple. + +<LI>Verify Location and Verify RNA Seq: These buttons are used to confirm that the data set correctly targets the last exon of <I>Grin2b</I>. Click on either link. The probe sequences used on the array are sent to the Genome Browser and the best match is found in real time using the BLAT algorithm. The Search Results page allows you to drill down to a view of the genome. Click on the "browser" link to the far left (top row). Look for the horizontal track that is made up of a series of black rectangles labeled "Blat Sequence" or "Probe XXXYYY". You will also see several "tracks" labeled <I>Grin2b</I> and <I>GRIN2B</I>. If you use the <B>Zoom Out 10X</B> button you will see that the probes and probe set are aligned with the 3' end of the last exon--a bit more detail than we had before. You may also notice that <I>Grin2b</I> is encoded on the minus strand of chromosome 6 and that the tiny arrow heads visible on the last intron point to the left (the transcription direction is from right to left). The Verify RNA seq button has the same function, but takes you to a GN mirror of the UCSC Browser that has added RNA sequencing data for brain, hippocampus, and eye (Jan 2011) of many BXD strains of mice. + +<LI>Basic Statistics: This button will generate summaries such as the average expression, the range, bar charts of expression ordered by strain and by rank. Try it quickly. + +<LI>Similar Traits: This button will provide you a link to <I>Grin2b</I> expression data in other data sets that may interest you. + +<LI>Probe Tool: A link to the sequence data for the individual probes that make up a probe set. This table can be used for a very fine-grained analysis of particular probe sets. + +<LI>Add to Collection: If you would like to add a trait to your collection of traits, transcripts, or markers, use this button. This is the same function we mentioned earlier. + +<LI> Reset: GN allows you to modify values for traits and this button is used to reset to the original values. +</OL> + +<p>In general, text that uses a blue font is also a link. For example, the text at the top of Figure 4 <A HREF="http://www.genenetwork.org/dbdoc/HC_M2_0606_P.html">Hippocampus Consortium M430v2 BXD (Jun06) PDNN</A> will link you to a Materials and Methods "metadata" or <B>Info</B> page. There is lots of information on the Info page, but the short summary is that the NR2B expression data in the Hippocampus mRNA database we are exploring was generated from approximately 1200 hippocampii and 600 mice belonging to 99 strains (typically three animals per array and approximately 200 arrays). This is one of the largest data sets in GN. Each array includes samples from a single age, sex, and litter. The BXD strain family were all made by crossing two parental strains, C57BL/6J and DBA/2J. Both of these parental strains have been fully sequenced. The Hippocampus data set includes expression estimates for both parental strain, and also data for 15 other common inbred strains, for example, 129S1/SvImJ, C3H/HeJ, CAST/EiJ, and others. There is also a complementary, but smaller Hippocampus Consortium data set for the CXB strains of mice.</p> + + +<p>Farther down the page we encounter sections labeled <B>Trait Correlations</B> and <b>Interval Mapping</b><span style='font-weight:normal'> and </span><b>Trait Data</b><span style='font-weight:normal'>. We will come back to these tools in a moment, but keep scrolling down to the actual numerical data on gene expression for <I>Grin2b</I>. + +The larger numbers in the boxes (6.631, 6.612, etc.) are estimates of the abundance of <i>Grin2b</i></span> mRNA in the hippocampii of different samples of mice. The smaller numbers (0.184, 0.205, etc.) are the standard errors of expression, usually based on two arrays (hence SEM also equals SD). Numbers are all expressed using a log base 2 scale. A value of 8 therefore corresponds to 2^8 or 256. A difference of one unit is roughly equivalent to a two-fold difference in expression in <i>Grin2b</i><span style='font-style:normal'> expression. DBA/2J has an expression of 6.506 +/- 0.008 whereas BXD14 has an expression of 7.604 +/- 0.232. That amounts to approximately a 2-fold difference in the amount of transcript. + +<P>These kinds of preliminary results often generate intriguing and testable hypothesis: do strains of mice have the anticipated differences in learning and memory performance given the known effects of <i>Grin2b</i> overexpression in transgenic mice? If you scroll down farther in this lists of <i>Grin2b</i><span style='font-style:normal'> expression estimates you will see that the strain of mouse called BXD80 only expresses 6.098 units of NR2B whereas BXD42 expresses 8.400 units. That amouts to a putative 5-fold difference in mRNA level. We need to take this with a grain of salt, because these expression estimates are lower than we expect. The average expression for all transcripts (including those NOT expressed) is 8 units. The fact that the average expression of the <I>Grin2b</I> probe set is less than average should make us worry. Are these data too noisy to use? Is there an unsuspected problem with the data handling or the probes? These are hard questions to answer but the <B>Probe Tool</B> is useful because you can look at the expression of the individual probes values used to generate the probe set summary value. We will skip this process for now, but remember that this "deeper" level is always just one click away. For the time being, let's evaluate the data using the Basic Statistics function. +</span></p> + +<p> <img width=572 height=351 src="/images/upload/Tutoral_Stats1.jpg" v:shapes="_x0000_i1031"> </p> +<p><B>Figure 5: Basic statistics for <I>Grin2b</I></B> + +<p><b>Step 5. Basic Statistics. </b><span style='font-weight:normal'>To get a better understanding of these values and how expression estimates are distributed click on the </span><b>Basic Statistics</b><span style='font-weight: normal'> button. A new window will open with a statistical summary table and a box plot toward the top (Figure 5), two bar charts in the middle, and a normal probability plot toward the bottom. You may not be familiar with these types of plots yet, but they are simple to read. The box plot is a simply summary of the spread of the 86 values. The blue plus sign represents the mean expression. The box defines the 25% and 75% quantiles (if we had studied exactly 100 strains these would be those strains at the 25 and 75 rank. If you want more information, just click on the link beneath the plot. + +The bar charts are easy to read. They provide a graphic output of the data that you saw in the Trait Data and Analysis Form. The Y axis of the graph is truncated and does not extend down to a value of zero. This tend to highlight the variation within strains. The error bars are quite large, and are only based on two samples (in this case the SEM is usually the same as the SD). Also note that the size of these error bars tend to increase as the expression increases (non-uniform error). High noise and non-uniform variance are all characteristics that should reduce your enthusiasm. But let's persevere, because these data have not yet cost you a penny and because this is a great lesson. + +<p> <img width=737 height=497 +src="/images/upload/Tutorial_Stats2.jpg" v:shapes="_x0000_i1031"> </p> +<p><B>Figure 6: Normal Probability plot for <I>Grin2b</I></B> + +<P>Toward the bottom of the Basic Statistics page you will find a Normal Probability plot (Figure 6). There is another link associated with this plot that will provide more background, but here is a brief explanation of how to read these plots. On the X axis is the expected Z score for every strain based on its ranking out of 86 strains. Values range from about -2.5 to +2.5. If you randomly drew 86 values from a normal distribution you would expect the lowest value to be about -2.5 standard deviations below the mean (or -2.5 Z) from the mean. The Y axis provides a read-out of the actual expression level. If the expression of NR2B were normally distributed then the strain averages would form a straight line. If expression of <I>Grin2b</I> were obviously controlled by a single Mendelian factor, then this plot would have an S shape with many high strains and many low strains and few strains with intermediate values. Instead this plot highlights skew toward low values (also seen in the box plot). A few strains have comparatively high expression, but the main feature is the excess of strains with values from 6.0 to 6.5 units. It does not look like a Mendelian trait. But looks can deceive. + +<P>What this plot also highlights is the wide range of expression of NR2B gene transcript in normal strains (the BXD strains are not mutant or knockout mice). But the high error raises the possibility that much of this variation is simply sampling error. If we performed an analysis of variance with Strain as our main effect, this data set would be associated with a modest and statistically insignificant F values. But we have other methods to evaluate this putative strain difference. We can map it and see if any interesting patterns emerge from the mapping that might cheer us up and demonstrate that the variation of strain means is actually true signal. In this case, the answer is (fortunately) a strong Yes (LOD = 16). But when you see data of this type, the usual answer will be No. + +<P>Variation in NR2B gene expression is a signal that we can now cautiously use to search for transcripts that co-vary. Does NR2B message covary with other subunits of the NMDA receptor complex (over 1000 transcripts are part of the postsynpatic density of which NR2B is a key member). Does the the expression of other genes compensate for the apparent 5-fold range in NR2B message level?</span></p> + +<p><b>Step 6. Covariation of expression.</b><span style='font-weight:normal'> To answer these types of questions return to the </span><b>Trait Data and Analysis Form</b><span style='font-weight:normal'> that has all of the values for <i>Grin2b</i></span> in 86 different strains of mice. This time select the <b>Trait Correlation</b><span style='font-weight:normal'> button. There are five pop-down menus that allow you to modify search parameters. + +Let's modify one of the default settings. Change <B>Return</B> to read <B>top 500</B>. The other seetings are fine for the time being.</span></p> Now click on the <B>Trait Correlations</B> button. + +<p> <img width=464 height=101 src="/images/upload/Tutorial_Correlation1.jpg" v:shapes="_x0000_i1032"> </p> +<p><B>Figure 7: How to set up the search for covariates of <I>Grin2b</I></B> + +<p>Within a few seconds of clicking this button, GN will return a new page of data, a<b> Correlation Table</b><span style='font-weight:normal'> of the top 499 transcripts that covary with variation in <i>Grin2b</i></span> expression. At the top of this list (sorted by p value) is <i>Grin2b</i><span style='font-style:normal'> itself. The third best covariate of our <I>Grin2b</I> probe set is another <I>Grin2b</I> probe set. That is reassuring. + +<P>Let's review the columns: + +<OL> +<span style='font-style:normal'> +<LI>The first column is just an index with check boxes. You can easily add items into your BXD Collection using these checkboxes. +<LI>Record ID: The ID of the trait; in this case just the probe set identifier given by Affymetrix +<LI>Symbol: The official gene symbol. Clicking on these symbols will link you to NCBI. +<LI>Description: The name of the trait or the name of the gene from which the mRNA is transcribed +<LI>Chr: The chromosome of the gene from which the transcript is transcribed +<LI>Megabase: The chromosomal nucleotide position of the most proximal end of the probe set (mm6 alignment) +<LI>Mean Expression: The average expression of the probe set (mean of strain averages) +<LI>Correlation: The correlation of with the reference trait, in this case with Grin2b probe set 1422223_at. +<LI>N Cases: The number of strains involved in the correlation analysis +<LI>p Value: The p value associated with the correlation and number of cases without correction for multiple tests. +<LI>Lit Corr: The Literature Correlation. This is a very cool column of data generated by Ramin Homayouni, Michael Berry and colleagues that summarizes the correlation of <I>Grin2b</I> with many other genes based upon an analysis of the PubMed Literature. +</OL> + +<P> + +<p> <img width=800 height=380 +src="/images/upload/Tutorial-Correlation2.jpg" v:shapes="_x0000_i1033"> </p> +<p"><B>Figure 8: Correlation Table</B> + +<P>Clicking on any correlation value will generate a scattergram of<i>Grin2b</i> on the X axis and the other transcript on the Y axis. For example, the scattergram of <i>Grin2B</i><span style='font-style:normal'> (X axis) versus <i>Grin2b</i> is shown in Figure 9. The </span><i>p</i><span style='font-style:normal'> value associated with this correlation is highly signficant and is listed in the upper right corner for both the parametric Pearson's r value and for Spearman's rank order r value. GN generates the <b>Correlation Table</b></span> after performing 45,100 statistical tests; so we should correct for multiple tests. In this case, the <i>p</i> value is significant even if we apply a stringent Bonferroni correction. You may regard this <I>Grin2b-to-Grin2b</I> correlation as somewhat of a disappointment, but the more you appreciate the great complexity of mRNA metabolism, the less suprised you will be. If you were planning follow-up functional or behavioral studies of strains with high and low <I>Grin2b</I> expression you would obviously want to resolve some of the discrepancies at the protein level or you could (with some risk) just select strains with high or low expression for all forms of <I>Grin2b</I> (BXD15, BXD24, BXD60 vs BXD14, BXD42, BXD96).</p> + +<P>Correlation Tables can be resorted. Click on the the small arrowheads in the header column to resort by the Literature Correlation. You will find that <I>Grin2b</I> actually does covary reasonably well with <I>Grin1</I> (r = 0.501). Generate the scatter plot for <I>Grin1</I> and <I>Grin2b</I>. + +<p> <img width=806 height=867 src="/images/upload/Tutorial_Correlation3.jpg" v:shapes="_x0000_i1034"> </p> +<p><B>Figure 9: Scatter plot of two probe sets that measure expression of different parts of <I>Grin2b</I>.</B> + +<p><b>Step 7. Gene ontology analysis.</b> At the top of the Correlation Table</b> is a button labeled <b>Gene Ontology</b>. When you click on this button GN sends a list of gene IDs to the WebGestalt server for analysis. Before you click on this button you need to decide which list of transcripts to send to WebGestalt. The easy answer is to send all 500 transcripts. To do this click on the <B>Select ALL</B> button. This action will highlight all 500 transcripts. Now click on the Gene Ontology button. The output will be a large graph consisting of three major categories and a "bush" of subcategories. </p> + + +<p> <img width=791 height=878 src="/images/upload/Tutorial_GO1.jpg" v:shapes="_x0000_i1035"> </p> +<p><B>Figure 10: Gene ontology analysis with WebGestalt</B> + + +<p>A gene ontology is a hierarchical categorization of genes by their functions. A large subset of the roughly 20000 genes measured using microarrays have been assigned to one or more functional categories. The three independent trunks of this ontology are "biological process", "molecular function", and "cellular component". Within each of the the GO category we see the number of genes included in this category and the p value. For example, for the category "Nervous System Development, the numbers are 21 genes with a p value of 0.005. You can click on the category and generate the list of all 21 genes--from <I>Acsl6</I> (the only covariate with a negative correlation) to <I>Ulk1</I>. The single category that has the highest "enrichment" is the molecular function "binding" with a p value of about 0.0000001. This category includes 261 of 500 transcripts on our <I>Grin2b</I> list. + +<b>Step 8: Mapping <I>Grin2b</I>.</b> At this point we have gained some confidence in the <I>Grin2b</I> expression data. While the expression values are low, they seem to be correctly associated with moleculates enriched in the postsynaptic complex. What causes the variation in <I>Grin2b</I> expression among strains of mice? The simple but unsatisfying answer is that differences are caused by <i>genetic variation between the parental strains that are inherited by the BXD progeny.</i></span> The WebQTL module of GN can give us much better answers. WebQTL can tell us where in the genome this genetic variation is located and which parental strain (C57BL/6J or DBA/2J) is associated with higher expression. These chromosomal regions are the ultimate, but most distal causes of variation in <i>Grin2b</i> mRNA abundance. These sources of variance can be mapped like any other genetically determined trait. The method we use to do this is called complex trait analysis or quantitative trait locus (QTL) mapping (hence the term WebQTL). The method is covered at an accessible level in a previous <a href="http://www.nervenet.org/papers/shortcourse98.html" target="_blank">SfN Short Course article</a>. + +<P>But now we will skip the details and proceed directly to the results. Go back to the <b>Trait Data and Analysis Form</b> and click on the <b>Interval Mapping</b><span style='font-weight:normal'> button.</span></p> + +<p> <img width=648 height=574 src="/images/upload/Tutorial_Map1.jpg" v:shapes="_x0000_i1038"> </p> +<p><B>Figure 11: QTL map for <I>Grin2b</I></B> + +<p>An <b>Interval Mapping Result</b><span style='font-weight:normal'> window will automatically open after a short pause during which WebQTL calculates and assembles results based on 4 million linear regression equations. The window should have to a single major spike on the right side of chromosome (Chr) 6. The X-axis is a linear representation of all mouse chromosomes, as if they were tied end to end (Chr 1 to the left, and Chr X to the far right). The Y-axis and the bold lines (blue) provide estimates of the likelihood that differences in NR2B expression are modulated by polymorphic loci (allelic variants). Likelihoods are presented using a chi square statistic called the likelihood ratio statistic (LRS). Big numbers are good in the sense that they signify that we have successfully identified a chromosomal interval that controls <i>Grin2b</i></span> expression. In this case, the number is extraordinarily high, with a peak LRS of 72.9 (LOD of 15.8) on Chr 6. The horizontal gray line and the and pink line are the statistical thresholds. If the spikes exceed the upper rose-colored line, then the linkage between the chromosomal interval and variation in <i>Grin2b</i><span style='font-style:normal'> expression is significant. In this case, only the Chr 6 linkage is significant, whereas that on Chr 4 at about 70 Mb is suggestive. </span></p> + +<p><b>Step 9. Evaluation of candidate genes. </b><span style='font-weight:normal'>Note that on the X-axis just under the largest spike there is a small purple triangle. This triangle indicates that genetic location of the <i>Grin2b</i></span> gene itself. The correspondence of the QTL and the location of the <I>Grin2b</I> gene suggest that polymorphisms in <i>Grin2b</i> modulate expression (for example, a variant in the <i>Grin2b</i> promoter). The finer jagged line (red or green) provides a gauge of whether DBA/2J (green) alleles or C57BL/6J (red) alleles contribute to higher expression of <I>Grin2</I>. See the far right axis to see how to read this "additive effect" scale. In this case, the allele or haplotype inherited from C57BL/J (red line) contributes to higher expression of <I>Grin2b</I>. Just to make sure, let's zoom in on the map of Chr 6 and confirm that the QTL does align with <I>Grin2b</I>. To zoom the map, click on the chromosome number (Chr 6) in the whole-genome interval map. This will generate a chromosome 6-specific map of <I>Grin2b</I> expression. Once you have this Chr 6 map on your screen, you can zoom again by clicking on the rose-colored horizontal bar at the top of the map. You will end up with a map that looks somewhat like Figure 11, in which the strongest position candidate is obviously <I>Grin2b</I> itself. We have informally "cloned" a QTL for <I>Grin2b</I> expresssion. </p> + +<p><span style='font-style:normal'><br> <img width=660 height=425 +src="/images/upload/Tutorial_Map2.jpg" v:shapes="_x0000_i1039"> </span></p> +<p><B>Figure 12: Zoomed QTL map for <I>Grin2b</I> on Chr 6</B> + + +<p>Having mapped the major controller of <I>Grin2b</I> expression, we can ask if any of the "left-over" variance can be explained by secondary QTLs. We can use either <B>Composite Interval Mapping</B> or the <B>Pair Scan</B> mapping function (to gain access to Composite Interval mapping you first need to click on the <B>Marker Regression</B> button). Both of these mapping methods are somewhat more advanced than simple interval mapping. Without going into the details (the data are weak), there is a hint that a region near the centromere of Chr 2 may also affect <I>Grin2b</I> expression by interacting non-additively with the Chr 6 variant of <I>Grin2b</I>. + + +<p><b>Conclusion. </b><span +style='font-weight:normal'>The tour you have just taken has led your through typical steps in analyzing and evaluating gene expression data. This tour may also have generated a number of intriguingand hypotheses about the relations of NR2B to itself and with molecules in the hippocampus. You can repeat this type of analysis with any of about 20000 other genes in this data set. You can do the same analysis for complex sets of transcript and traits. you can also repeat this type of analysis in other tissues. It takes time, but the cost-benefit ratio is high.</span></p> + + +<p><b>Step 10. A simple self-test</b></p> + <p>Question1. Can you verify any of these NR2B results using a different data set such as the SJUT Cerebellum M430 data set? What does a success or failure indicate?</p> + + +<p>Q2. Are there any functionally interesting correlations between <i>Grin2b</i><span style='font-style:normal'> expression and behavioral traits in these same strains of mice? (Hint: generate a <b>Correlation Table </b></span>of <i>Grin2b</i><span style='font-style:normal'> with traits in the <b>Published Phenotypes</b></span> database.) What is the importance of a correlation and what mechanisms can generated these correlations? Can very high correlations still be entirely spurious? </p> + +<p>Q3. Do NR1 (<i>Grin1</i><span style='font-style: +normal'>) and NR2B (</span><i>Grin2b</i><span style='font-style:normal'>) share common modulators on Chr 8?</span></p> + + +<p><b>Caveat emptor: </b><span style='font-weight:normal'>Always be skeptical regarding results. There are pitfalls of this type of analysis highlighted in some of the questions above. These are more than counterbalanced by tremendous opportunities. Consider GN as a great tool to generate interesting new hypotheses, and be prepared to validate or refute these hypotheses using independent data and direct experimental tests.</span></p> + +<p>--------</p> + +<p>ANSWERS:<b> Q1.</b><span style='font-weight:normal'> No, verification is not possible using the Cerebellum data set. Different tissues have different expression patterns and control. </span> + +<b>Q2.</b><span style='font-weight:normal'> Yes, you should get a high correlation with <i>rearing movements after a cocaine injection</i></span> (a paper by B. Jones et al., 1999). Yes, very high correlations can be "functionally" spurious and can arise from linkage disequilibrium, sampling error, or (we hope rarely) poor experimental design. + +<b>Q3.</b> No. + + +<p>This work was supported by a Human Brain Project funded jointly by the National Institute on Drug Abuse, National Institute of Mental Health, the National Institute on Alcohol Abuse and Alcoholism, and the National Science Foundation (award P20-MH 62009 and P20-DA 21131 to KFM and RW) and by a separate grant from The National Institute on Alcohol Abuse and Alcoholism (INIA grants U01AA13499, U24AA13513 to RW).</p> + +<p><span style='color:black'>(Text version of March 28, 2011 by RW</span></p> + +<!-- +<p><span style='color:black'>(Text generated October 8, 2003 by RW; modified Oct. 27, 2003 by RW; completely rewritten by RW on May 22, 2006.)</span></p> +--> + + + + +</TR> +</TABLE> +</TD> +</TR> + +<TR> +<TD align=center bgColor=#ddddff class="solidBorder"> +<!--Start of footer--> +<TABLE width="90%"> +<script language='JavaScript' src='/javascript/footer.js'></script> +</TABLE> +<!--End of footer--> +</TD> +</TR> +</TBODY> +</TABLE><!-- /Footer --> + +<!-- menu script itself. you should not modify this file --> +<script language="JavaScript" src="/javascript/menu_new.js"></script> +<!-- items structure. menu hierarchy and links are stored there --> +<script language="JavaScript" src="/javascript/menu_items.js"></script> + +<!-- files with geometry and styles structures --> +<script language="JavaScript" src="/javascript/menu_tpl.js"></script> +<script language="JavaScript"> +<!--// +// Note where menu initialization block is located in HTML document. +// Don't try to position menu locating menu initialization block in +// some table cell or other HTML element. Always put it before </body> +// each menu gets two parameters (see demo files) +// 1. items structure +// 2. geometry structure +new menu (MENU_ITEMS, MENU_POS); +// make sure files containing definitions for these variables are linked to the document +// if you got some javascript error like "MENU_POS is not defined", then you've made syntax +// error in menu_tpl.js file or that file isn't linked properly. + +// also take a look at stylesheets loaded in header in order to set styles +//--> + +</script> +</BODY> +</HTML> diff --git a/web/tutorial/movies/index.html b/web/tutorial/movies/index.html new file mode 100755 index 00000000..6af90770 --- /dev/null +++ b/web/tutorial/movies/index.html @@ -0,0 +1,105 @@ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> +<HTML><HEAD><TITLE>GeneNetwork Demos</TITLE> +<META http-equiv=Content-Type content="text/html; charset=iso-8859-1"> + +<LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'> +<LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'> +<link rel="stylesheet" media="all" type="text/css" href="/css/tabbed_pages.css" /> +<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT> + +<SCRIPT SRC="/javascript/dhtml.js"></SCRIPT> + +<script src="/javascript/tabbed_pages.js" type="text/javascript"></script> + +</HEAD> +<BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff> +<TABLE cellSpacing=5 cellPadding=4 width="100%" border=0> +<TBODY> +<TR> +<script language="JavaScript" src="/javascript/header.js"></script> +</TR> +<TR> +<TD bgColor=#eeeeee class="solidBorder"> +<Table width= "100%" cellSpacing=0 cellPadding=5><TR> +<!-- Body Start from Here --> +<TD valign="top" height="200" width="100%" bgcolor="#eeeeee"> +<P class="title">GeneNetwork Tutorials <A HREF="/webqtl/main.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A></P> + + +<P class="subtitle">Movies:</P> +<Blockquote> +<P></P> +<P> +<table border="0" cellpadding="0" cellspacing="0" bgcolor="#000000"> +<tr><td> +<table border="0" cellpadding="5" cellspacing="1" align="left"> +<tr bgcolor="e4e4ff"> +<td><font color=#000000><center>Introduction to GeneNetwork</center></font></td> +</tr> +<tr bgcolor="#eeeeee"> +<td> +<iframe width="560" height="315" src="http://www.youtube.com/embed/B3g_0q-ldJ8" frameborder="0" allowfullscreen></iframe> +</center></font></td> +</tr> + +</table> + +</td> +</tr> +</table> +</Blockquote> +</P> + + + +<!--<P class="subtitle">Information about this text file:</P> +<Blockquote> +<P>This file last updated by A.Centeno on 1-25-2011</P> +</Blockquote>--> + +</TR></TABLE> +</TD> +</TR> +<TR> +<TD align=center bgColor=#ddddff class="solidBorder"> +<!--Start of footer--> +<TABLE width="90%"> +<script language='JavaScript' src='/javascript/footer.js'></script> +<TR> +<TD colspan=3 class="fs12"> +<UL> + +</UL> +</TD> +</TR> +</TABLE> +<!--End of footer--> +</TD> +</TR> +</TABLE> +<!-- /Footer --> +<!-- menu script itself. you should not modify this file --> +<script language="JavaScript" src="/javascript/menu_new.js"></script> +<!-- items structure. menu hierarchy and links are stored there --> +<script language="JavaScript" src="/javascript/menu_items.js"></script> +<!-- files with geometry and styles structures --> +<script language="JavaScript" src="/javascript/menu_tpl.js"></script> +<script language="JavaScript"> +<!--// +// Note where menu initialization block is located in HTML document. +// Don't try to position menu locating menu initialization block in +// some table cell or other HTML element. 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id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Robots content=NoIndex> <link rel=Stylesheet href="master03_stylesheet.css"> <script language=JavaScript src=script.js></script> +<script> +<!-- + parent.location.href=document.all.item("Main-File").href +//--> +</script> + </head> <body> <div class=O style='text-align:right;position:absolute;top:.53%;left:58.01%; width:40.79%;height:2.12%'><span style='color:black'><b>Memphis Microarray 2003</b></span></div> <div class=O style='position:absolute;top:97.52%;left:1.32%;width:42.78%; height:2.12%'><span style='color:black'><b>June 11, 2003, Rob Williams</b></span></div> <div class=O style='text-align:right;position:absolute;top:97.52%;left:58.01%; width:40.79%;height:2.12%'><span 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none;}--> </style> </head> <body bgcolor=black text=white link=white vlink=white alink=white onload=" parent.base.highlite();" onresize="self.location.reload();"> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID1 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p1" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('1')" id=AREF>WebQTL Demonstration One<br> please link to <br> www.webqtl.org/search.html</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID2 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p2" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('2')" id=AREF>"or webqtl.org/search.html..."</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID3 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p3" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('3')" id=AREF>Search results</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID4 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p4" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('4')" id=AREF>"First page of data:"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID5 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p5" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('5')" id=AREF>"Data sources:"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID6 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p6" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('6')" id=AREF>"Return to Trait Data page"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID7 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p7" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('7')" id=AREF>"Discovering shared expression patterns"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID8 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p8" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('8')" id=AREF>"The App transcript neighborhood"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID9 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p9" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('9')" id=AREF>"Handdrawn sketch of the neighborhood"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID10 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p10" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('10')" id=AREF>"What a network is likely..."</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID11 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p11" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('11')" id=AREF>Are there experimental results to corroborate a link between App with Hsp84-1?</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID12 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p12" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('12')" id=AREF>"2.45 billion scatter plots"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID13 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p13" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('13')" id=AREF>"Cross-tissue type correlations"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID14 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p14" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('14')" id=AREF>"Cross-modal correlations:"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID15 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p15" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('15')" id=AREF>WebQTL<span style="mso-spacerun: yes"> </span><br> link to <br> www.webqtl.org/search.html</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID16 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p16" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('16')" id=AREF>Slide 16</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID17 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p17" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('17')" id=AREF>Slide 17</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID18 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p18" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('18')" id=AREF>WebQTL to exploring upstream control</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID19 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p19" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('19')" id=AREF>WebQTL to exploring upstream control.</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID20 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p20" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('20')" id=AREF>The whole neighborhood is modulated!</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID21 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p21" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('21')" id=AREF>Which gene is the QTL?</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID22 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p22" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('22')" id=AREF>Slide 22</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID23 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p23" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('23')" id=AREF>Slide 23</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID24 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p24" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('24')" id=AREF>Tissue differences in probe performance</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID25 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p25" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('25')" id=AREF>Is there known biology to link Hars2 with App?</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID26 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p26" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('26')" id=AREF>WebQTL<span style="mso-spacerun: yes"> </span><br> link to <br> www.webqtl.org/search.html</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID27 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p27" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('27')" id=AREF>Requirement: The gene must be polymorphic to be genetically ÒupstreamÓ</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID28 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p28" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('28')" id=AREF>Direct correlations between genotypes and traits</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID29 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p29" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('29')" id=AREF>WhatÕs downstream of Chr 2 near Hars2?</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID30 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p30" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('30')" id=AREF>WhatÕs downstream of Chr 2 near Hars2?</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID31 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p31" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('31')" id=AREF>Does Hars2 correlate with Actn2 strongly?</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID32 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p32" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('32')" id=AREF>Contact for comments and improvements:</a></b></font></td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/outline_expand.gif b/web/tutorial/ppt/WebQTLDemo_files/outline_expand.gif new file mode 100755 index 00000000..c8c72b13 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/outline_expand.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/outline_expanded.htm b/web/tutorial/ppt/WebQTLDemo_files/outline_expanded.htm new file mode 100755 index 00000000..3e6bdf31 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/outline_expanded.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Robots content=NoIndex> <style> <!--a {text-decoration: none;}--> </style> </head> <body bgcolor=black text=white link=white vlink=white alink=white onload=" parent.base.highlite();" onresize="self.location.reload();"> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID1 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p1" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('1')" id=AREF>WebQTL Demonstration One<br> please link to <br> www.webqtl.org/search.html</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Part 1: How to discover shared expression patterns (slides 2Ð14)</font></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Part 2. Discovering upstream modulators (15Ð25)</font></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Discovering downstream targets</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID2 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p2" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('2')" id=AREF>"or webqtl.org/search.html..."</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>or webqtl.org/search.html (mirror)</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID3 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p3" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('3')" id=AREF>Search results</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID4 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p4" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('4')" id=AREF>"First page of data:"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>First page of data: The ÒTrait Data FormÓ</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID5 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p5" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('5')" id=AREF>"Data sources:"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Data sources: Phenotpyes and genotypes</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID6 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p6" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('6')" id=AREF>"Return to Trait Data page"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Return to Trait Data page</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID7 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p7" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('7')" id=AREF>"Discovering shared expression patterns"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Discovering shared expression patterns</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID8 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p8" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('8')" id=AREF>"The App transcript neighborhood"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>The App transcript neighborhood</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID9 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p9" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('9')" id=AREF>"Handdrawn sketch of the neighborhood"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Handdrawn sketch of the neighborhood</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID10 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p10" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('10')" id=AREF>"What a network is likely..."</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>What a network is likely to look like (but App will not be center of universe).</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID11 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p11" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('11')" id=AREF>Are there experimental results to corroborate a link between App with Hsp84-1?</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID12 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p12" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('12')" id=AREF>"2.45 billion scatter plots"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>2.45 billion scatter plots: here is one of the best</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID13 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p13" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('13')" id=AREF>"Cross-tissue type correlations"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Cross-tissue type correlations</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID14 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p14" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('14')" id=AREF>"Cross-modal correlations:"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Cross-modal correlations: From mRNA to to anatomy and to behavior and pharmacology</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID15 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p15" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('15')" id=AREF>WebQTL<span style="mso-spacerun: yes"> </span><br> link to <br> www.webqtl.org/search.html</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Discovering shared expression patterns</font></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Discovering upstream modulators (QTLs)</font></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Discovering downstream targets</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID16 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p16" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('16')" id=AREF>Slide 16</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID17 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p17" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('17')" id=AREF>Slide 17</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID18 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p18" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('18')" id=AREF>WebQTL to exploring upstream control</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID19 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p19" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('19')" id=AREF>WebQTL to exploring upstream control.</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID20 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p20" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('20')" id=AREF>The whole neighborhood is modulated!</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID21 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p21" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('21')" id=AREF>Which gene is the QTL?</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID22 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p22" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('22')" id=AREF>Slide 22</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID23 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p23" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('23')" id=AREF>Slide 23</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID24 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p24" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('24')" id=AREF>Tissue differences in probe performance</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID25 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p25" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('25')" id=AREF>Is there known biology to link Hars2 with App?</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID26 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p26" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('26')" id=AREF>WebQTL<span style="mso-spacerun: yes"> </span><br> link to <br> www.webqtl.org/search.html</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Discovering shared expression patterns</font></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Discovering upstream modulators (QTLs)</font></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Discovering downstream targets</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID27 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p27" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('27')" id=AREF>Requirement: The gene must be polymorphic to be genetically ÒupstreamÓ</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID28 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p28" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('28')" id=AREF>Direct correlations between genotypes and traits</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID29 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p29" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('29')" id=AREF>WhatÕs downstream of Chr 2 near Hars2?</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID30 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p30" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('30')" id=AREF>WhatÕs downstream of Chr 2 near Hars2?</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID31 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p31" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('31')" id=AREF>Does Hars2 correlate with Actn2 strongly?</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID32 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p32" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('32')" id=AREF>Contact for comments and improvements:</a></b></font></td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/outline_navigation_bar.htm b/web/tutorial/ppt/WebQTLDemo_files/outline_navigation_bar.htm new file mode 100755 index 00000000..06c789c8 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/outline_navigation_bar.htm @@ -0,0 +1,37 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); 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+var gCurSld = gPrevSld = 1, g_offset = 0, gNtsOpen = gHasNts = gOtlTxtExp = gNarrationPaused = false, gOtlOpen = true +window.gPPTHTML=SupportsPPTHTML() +var g_hideNav = 0; +function UpdNtsPane(){ PPTNts.location.replace( MHTMLPrefix+GetHrefObj( gCurSld ).mNtsHref ) } +function UpdNavPane( sldIndex ){ if(gNavLoaded) PPTNav.UpdNav() } +function UpdOtNavPane(){ if(gOtlNavLoaded) PPTOtlNav.UpdOtlNav() } +function UpdOtlPane(){ if(gOtlLoaded) PPTOtl.UpdOtl() } +function SetHasNts( fVal ) +{ + if( gHasNts != fVal ) { + gHasNts=fVal + UpdNavPane() + } +} + +function ToggleVNarration() +{ + if ( base.msie < 0 ) { + PPTSld.ToggleSound( false, PPTSld.document.NSPlay ); + return; + } + + rObj=PPTSld.document.all("NSPlay") + if( rObj ) { + if( gNarrationPaused ) + rObj.Play() + else + rObj.Pause() + + gNarrationPaused=!gNarrationPaused + } +} + +function PrevSldViewed(){ GoToSld( GetHrefObj(gPrevSld).mSldHref ) } +function HasPrevSld() { return ( gIsEndShow || ( g_currentSlide != 1 && GetHrefObj( g_currentSlide-1 ).mVis == 1 )||( GetCurrentSlideNum() > 1 ) ) } +function HasNextSld() { return (GetCurrentSlideNum() != GetNumSlides()) } +function StartEndShow() +{ +// g_hideNav = 1; +// PPTNav.location.reload(); + if( PPTSld.event ) PPTSld.event.cancelBubble=true + + doc=PPTSld.document + doc.open() + doc.writeln('<html><head><script > /*defer>*/ g_ctxmenu = 0; ' + + 'if( parent.base.msie < 0 ) { document.captureEvents(Event.KEYPRESS); document.captureEvents(Event.MOUSEDOWN); document.onkeypress = _KPH; document.onmousedown = _KPH; } ' + + 'function DocumentOnClick(event) { return _KPH(event); } function IsContextMenu() { return (g_ctxmenu ==1); } ' + + 'function _KPH(event)' + + '{ ' + + 'if ( parent.base.msie < 0 && (parent.IsFullScrMode() ) && event ) { if ( (!parent.IsMac() && event.which == 3) || ( parent.IsMac() && (event.modifiers & Event.CONTROL_MASK) && event.which == 1 ) ) { return parent.KPH(event); } ' + + ' else if (event.which == 27 || event.which == 32 || event.which == 13 || parent.HitOK( event ) || (event.which == 78) || (event.which == 110) || (event.which == 29) || (event.which == 31) || (event.which == 12) ) { if ( IsContextMenu() ) { return parent.KPH(event); } parent.base.CloseFullScreen(); return; } ' + + ' else if ( (event.which == 80) || (event.which == 112) || (event.which == 30) || (event.which == 28) || (event.which == 11) || (event.which == 8) ) { parent.M_GoPrevSld(); } } ' + + 'if( parent.HideMenu() ) return; if( (parent.IsFullScrMode() ) && event) { if ( (event.keyCode==27 || event.keyCode == 13 || event.keyCode==32 || event.type=="click" ) || (event.keyCode == 78) || (event.keyCode == 110) ) { parent.base.CloseFullScreen(); }' + + ' else if ( (event.keyCode == 80) || (event.keyCode == 112) ) { parent.M_GoPrevSld(); } } } function Unload() { parent.gIsEndShow=0; } function SetupEndShow() { if ( !parent.IsFullScrMode() ) { return; } else { parent.PPTNav.location.reload(); } parent.gIsEndShow=1; if ( parent.g_docTable[0].type != "jpeg" ) { if ( parent.base.msie < 0 ) {parent.createCM(); } document.oncontextmenu=parent._CM; } }</script></head><body scroll=\"no\" onclick=\"DocumentOnClick(event)\" onkeypress=\"_KPH(event)\" bgcolor=\"black\" onload=\"SetupEndShow()\" onunload=\"Unload()\"><center><p><font face=Tahoma color=white size=2><br><b>' + ENDSHOW_MESG + '</b></font></p></center></body></html>') + doc.close() +} +function SetSldVisited(){ gDocTable[gCurSld-1].mVisited=true } +function IsSldVisited(){ return gDocTable[gCurSld-1].mVisited } +function hrefList( sldHref, visible, sldIdx ) +{ + this.mSldHref= this.mNtsHref = sldHref + this.mSldIdx = sldIdx + this.mOrigVis= this.mVis = visible + this.mVisited= false +} +var gDocTable = new Array( + new hrefList("slide0001.htm", 1, 1), + new hrefList("slide0002.htm", 1, 2), + new hrefList("slide0003.htm", 1, 3), + new hrefList("slide0004.htm", 1, 4), + new hrefList("slide0005.htm", 1, 5), + new hrefList("slide0006.htm", 1, 6), + new hrefList("slide0007.htm", 1, 7), + new hrefList("slide0008.htm", 1, 8), + new hrefList("slide0009.htm", 1, 9), + new hrefList("slide0010.htm", 1, 10), + new hrefList("slide0011.htm", 1, 11), + new hrefList("slide0012.htm", 1, 12), + new hrefList("slide0013.htm", 1, 13), + new hrefList("slide0014.htm", 1, 14), + new hrefList("slide0015.htm", 1, 15), + new hrefList("slide0016.htm", 1, 16), + new hrefList("slide0017.htm", 1, 17), + new hrefList("slide0018.htm", 1, 18), + new hrefList("slide0019.htm", 1, 19), + new hrefList("slide0020.htm", 1, 20), + new hrefList("slide0021.htm", 1, 21), + new hrefList("slide0022.htm", 1, 22), + new hrefList("slide0023.htm", 1, 23), + new hrefList("slide0024.htm", 1, 24), + new hrefList("slide0025.htm", 1, 25), + new hrefList("slide0026.htm", 1, 26), + new hrefList("slide0027.htm", 1, 27), + new hrefList("slide0028.htm", 1, 28), + new hrefList("slide0029.htm", 1, 29), + new hrefList("slide0030.htm", 1, 30), + new hrefList("slide0031.htm", 1, 31), + new hrefList("slide0032.htm", 1, 32) +); + +function ImgBtn( oId,bId,w,action ) +{ + var t=this + t.Perform = _IBP + t.SetActive = _IBSetA + t.SetInactive= _IBSetI + t.SetPressed = _IBSetP + t.SetDisabled= _IBSetD + t.Enabled = _IBSetE + t.ChangeIcon = null + t.UserAction = action + t.ChgState = _IBUI + t.mObjId = oId + t.mBorderId= bId + t.mWidth = w + t.mIsOn = t.mCurState = 0 +} +function _IBSetA() +{ + if( this.mIsOn ) { + obj=this.ChgState( gHiliteClr,gShadowClr,2 ) + obj.style.posTop=0 + } +} +function _IBSetI() +{ + if( this.mIsOn ) { + obj=this.ChgState( gFaceClr,gFaceClr,1 ) + obj.style.posTop=0 + } +} +function _IBSetP() +{ + if( this.mIsOn ) { + obj=this.ChgState( gShadowClr,gHiliteClr,2 ) + obj.style.posLeft+=1; obj.style.posTop+=1 + } +} +function _IBSetD() +{ + obj=this.ChgState( gFaceClr,gFaceClr,0 ) + obj.style.posTop=0 +} +function _IBSetE( state ) +{ + var t=this + GetObj( t.mBorderId ).style.visibility="visible" + if( state != t.mIsOn ) { + t.mIsOn=state + if( state ) + t.SetInactive() + else + t.SetDisabled() + } +} +function _IBP() +{ + var t=this + if( t.mIsOn ) { + if( t.UserAction != null ) + t.UserAction() + if( t.ChangeIcon ) { + obj=GetObj(t.mObjId) + if( t.ChangeIcon() ) + obj.style.posLeft=obj.style.posLeft+(t.mCurState-4)*t.mWidth + else + obj.style.posLeft=obj.style.posLeft+(t.mCurState-0)*t.mWidth + } + t.SetActive() + } +} +function _IBUI( clr1,clr2,nextState ) +{ + var t=this + SetBorder( GetObj( t.mBorderId ),clr1,clr2 ) + obj=GetObj( t.mObjId ) + obj.style.posLeft=obj.style.posLeft+(t.mCurState-nextState)*t.mWidth-obj.style.posTop + t.mCurState=nextState + return obj +} +function TxtBtn( oId,oeId,action,chkState ) +{ + var t=this + t.Perform = _TBP + t.SetActive = _TBSetA + t.SetInactive= _TBSetI + t.SetPressed = _TBSetP + t.SetDisabled= _TBSetD + t.SetEnabled = _TBSetE + t.GetState = chkState + t.UserAction = action + t.ChgState = _TBUI + t.mObjId = oId + t.m_elementsId= oeId + t.mIsOn = 1 +} +function _TBSetA() +{ + var t=this + if( t.mIsOn && !t.GetState() ) + t.ChgState( gHiliteClr,gShadowClr,0,0 ) +} +function _TBSetI() +{ + var t=this + if( t.mIsOn && !t.GetState() ) + t.ChgState( gFaceClr,gFaceClr,0,0 ) +} +function _TBSetP() +{ + if( this.mIsOn ) + this.ChgState( gShadowClr,gHiliteClr,1,1 ) +} +function _TBSetD() +{ + this.ChgState( gFaceClr,gFaceClr,0,0 ) + this.mIsOn = 0 +} +function _TBSetE() +{ + var t=this + if( !t.GetState() ) + t.ChgState( gFaceClr,gFaceClr,0,0 ) + else + t.ChgState( gShadowClr,gHiliteClr,1,1 ) + t.mIsOn = 1 +} +function _TBP() +{ + var t=this + if( t.mIsOn ) { + if( t.UserAction != null ) + t.UserAction() + if( t.GetState() ) + t.SetPressed() + else + t.SetActive() + } +} +function _TBUI( clr1,clr2,lOffset,tOffset ) +{ + SetBorder( GetObj( this.mObjId ),clr1,clr2 ) + Offset( GetObj( this.m_elementsId ),lOffset,tOffset ) +} +function GetObj( objId ){ return document.all.item( objId ) } +function Offset( obj, top, left ){ obj.style.top=top; obj.style.left=left } +function SetBorder( obj, upperLeft, lowerRight ) +{ + s=obj.style; + s.borderStyle = "solid" + s.borderWidth = 1 + s.borderLeftColor = s.borderTopColor = upperLeft + s.borderBottomColor= s.borderRightColor = lowerRight +} +function GetBtnObj(){ return gBtnArr[window.event.srcElement.id] } +function BtnOnOver(){ b=GetBtnObj(); if( b != null ) b.SetActive() } +function BtnOnDown(){ b=GetBtnObj(); if( b != null ) b.SetPressed() } +function BtnOnOut(){ b=GetBtnObj(); if( b != null ) b.SetInactive() } +function BtnOnUp() +{ + b=GetBtnObj() + if( b != null ) + b.Perform() + else + Upd() +} +function GetNtsState(){ return parent.gNtsOpen } +function GetOtlState(){ return parent.gOtlOpen } +function GetOtlTxtState(){ return parent.gOtlTxtExp } +function NtsBtnSetFlag( fVal ) +{ + s=document.all.item( this.m_flagId ).style + s.display="none" + if( fVal ) + s.display="" + else + s.display="none" +} + +var gHiliteClr="THREEDHIGHLIGHT",gShadowClr="THREEDSHADOW",gFaceClr="THREEDFACE" +var gBtnArr = new Array() +gBtnArr["nb_otl"] = new TxtBtn( "nb_otl","nb_otlElem",parent.ToggleOtlPane,GetOtlState ) +gBtnArr["nb_nts"] = new TxtBtn( "nb_nts","nb_ntsElem",parent.ToggleNtsPane,GetNtsState ) +gBtnArr["nb_prev"]= new ImgBtn( "nb_prev","nb_prevBorder",30,parent.GoToPrevSld ) +gBtnArr["nb_next"]= new ImgBtn( "nb_next","nb_nextBorder",30,parent.GoToNextSld ) +gBtnArr["nb_sldshw"]= new ImgBtn( "nb_sldshw","nb_sldshwBorder",18,parent.FullScreen ) +gBtnArr["nb_voice"] = new ImgBtn( "nb_voice","nb_voiceBorder",18,parent.ToggleVNarration ) +gBtnArr["nb_otlTxt"]= new ImgBtn( "nb_otlTxt","nb_otlTxtBorder",23,parent.ToggleOtlText ) +gBtnArr["nb_nts"].m_flagId= "notes_flag" +gBtnArr["nb_nts"].SetFlag = NtsBtnSetFlag +gBtnArr["nb_otlTxt"].ChangeIcon= GetOtlTxtState +var sNext="Next",sPrev="Previous",sEnd="End Show",sFont="Arial", alwaysOn = false +function ShowMenu() +{ + BuildMenu(); + var doc=PPTSld.document.body,x=PPTSld.event.clientX+doc.scrollLeft,y=PPTSld.event.clientY+doc.scrollTop + + m = PPTSld.document.all.item("ctxtmenu") + m.style.pixelLeft=x + if( (x+m.scrollWidth > doc.clientWidth)&&(x-m.scrollWidth > 0) ) + m.style.pixelLeft=x-m.scrollWidth + + m.style.pixelTop=y + if( (y+m.scrollHeight > doc.clientHeight)&&(y-m.scrollHeight > 0) ) + m.style.pixelTop=y-m.scrollHeight + + m.style.display="" +} +function _CM() +{ + if( !parent.IsFullScrMode() && !alwaysOn) return; + + if(!PPTSld.event.ctrlKey) { + ShowMenu() + return false + } else + HideMenu() +} + +function processNavKPH(event) { + if ( PPTSld && (event.keyCode != 13 || !event.srcElement.href || event.srcElement.href == "" ) ) + return PPTSld._KPH(event); +} +function processNavClick() { + HideMenu(); + return true; +} +function BuildMenu() +{ + if( PPTSld.document.all.item("ctxtmenu") ) return + + var mObj=CreateItem( PPTSld.document.body ) +mObj.id="ctxtmenu" + var s=mObj.style + s.position="absolute" + s.cursor="default" + s.width="100px" + SetCMBorder(mObj,"menu","black") + + var iObj=CreateItem( mObj ) + SetCMBorder( iObj, "threedhighlight","threedshadow" ) + iObj.style.padding=2 + if ( self.IsFullScrMode() ) { + CreateMenuItem( iObj,sNext,M_GoNextSld,M_True ) + CreateMenuItem( iObj,sPrev,M_GoPrevSld,M_HasPrevSld ) + } + else { + CreateMenuItem( iObj,sNext, base.TP_GoToNextSld, base.HasNextSld ) + CreateMenuItem( iObj,sPrev,base.GoToPrevSld, base.HasPrevSld ) + } + var sObj=CreateItem( iObj ) + SetCMBorder(sObj,"menu","menu") + var s=sObj.style + s.borderTopColor="threedshadow" + s.borderBottomColor="threedhighlight" + s.height=1 + s.fontSize="0px" + if ( self.IsFullScrMode() ) + CreateMenuItem( iObj,sEnd,M_End,M_True ) + else + CreateMenuItem( iObj,sEnd,M_End,M_False ) +} +function Highlight() { ChangeClr("activecaption","threedhighlight") } +function Deselect() { ChangeClr("threedface","menutext") } +function Perform() +{ + e=PPTSld.event.srcElement + if( e.type=="menuitem" && e.IsActive() ) + e.Action() + else + PPTSld.event.cancelBubble=true +} +function ChangeClr( bg,clr ) +{ + e=PPTSld.event.srcElement + if( e.type=="menuitem" && e.IsActive() ) { + e.style.backgroundColor=bg + e.style.color=clr + } +} + +function M_HasPrevSld() { return( base.HasPrevSld() ) } +function M_GoNextSld() { + base.SetFSMode(1); + if( gIsEndShow ) + M_End(); + else { + if ( base.HasNextSld() ) + base.GoToNextSld(); + else if ( base.EndSlideShow ) { + StartEndShow(); + gIsEndShow = 1; + + PPTNav.location.reload(); + } + else + base.CloseFullScreen(); + } +} +function M_GoPrevSld() { + base.SetFSMode(1); + g_hideNav = 0; + if( gIsEndShow ) { + gIsEndShow = 0; + if ( base.msie > 0 && IsMac() ) + ChangeFrame( SLIDE_FRAME, GetHrefObj( g_currentSlide ).m_slideHref ); + else + PPTSld.history.back(); + + PPTNav.location.reload(); + if( PPTSld.event ) + PPTSld.event.cancelBubble=true; + } + else + base.GoToPrevSld(); +} +function M_True() { return true } +function M_False() { return false } + +function M_End() { + base.CloseFullScreen(); + /*PPTSld.event.cancelBubble=true; + window.close( self )*/ +} + +function CreateMenuItem( node,text,action,eval ) +{ + var e=CreateItem( node ) + e.type="menuitem" + e.Action=action + e.IsActive=eval + e.innerHTML=text + + if( !e.IsActive() ) + e.style.color="threedshadow" + e.onclick=Perform + e.onmouseover=Highlight + e.onmouseout=Deselect + s=e.style; + s.fontFamily=sFont + s.fontSize="8pt" + s.paddingLeft=2 +} +function CreateItem( node ) +{ + var elem=PPTSld.document.createElement("DIV") + node.insertBefore( elem ) + return elem +} +function SetCMBorder( o,ltClr,rbClr ) +{ + var s=o.style + s.backgroundColor="menu" + s.borderStyle="solid" + s.borderWidth=1 + s.borderColor=ltClr+" "+rbClr+" "+rbClr+" "+ltClr +} + +/* netscape context menu */ +g_ctxmenu = 0; +function setRect( obj, X, Y, W, H ) { + obj.top = Y; + obj.left = X; + obj.clip.top = 0; + obj.clip.left = 0; + obj.clip.bottom = H; + obj.clip.right = W; +} + +function KPH(event) { + if ( ! base.IsFullScrMode() && !alwaysOn ) + return true; + + if ( (!IsMac() &&event.which == 3) || ( IsMac() && (event.modifiers & Event.CONTROL_MASK) && event.which == 1 ) ) { + PPTSld.g_ctxmenu = 1; + PPTSld.stripUobj.visibility = "show"; + PPTSld.stripDobj.visibility = "show"; + PPTSld.shadeUobj.visibility = "show"; + PPTSld.shadeDobj.visibility = "show"; + PPTSld.panelobj.visibility = "show"; + PPTSld.Fobj.visibility = "show"; + PPTSld.Bobj.visibility = "show"; + PPTSld.Eobj.visibility = "show"; + + setRect(PPTSld.shadeUobj, event.pageX-2, event.pageY-2, 82, 67 ); + setRect(PPTSld.shadeDobj, event.pageX, event.pageY, 82, 67 ); + setRect(PPTSld.panelobj, event.pageX, event.pageY, 80, 65 ); + setRect(PPTSld.Fobj, event.pageX, event.pageY, 80, 20 ); + setRect(PPTSld.Bobj, event.pageX, event.pageY+20, 80, 20 ); + setRect(PPTSld.stripUobj, event.pageX, event.pageY+41, 80, 1 ); + setRect(PPTSld.stripDobj, event.pageX, event.pageY+43, 80, 1 ); + setRect(PPTSld.Eobj, event.pageX, event.pageY+45, 80, 20 ); + return false; + } + if ( HitOK( event ) ) { + PPTSld.g_ctxmenu = 0; + PPTSld.stripUobj.visibility = "hide"; + PPTSld.stripDobj.visibility = "hide"; + PPTSld.shadeUobj.visibility = "hide"; + PPTSld.shadeDobj.visibility = "hide"; + PPTSld.panelobj.visibility = "hide"; + PPTSld.Fobj.visibility = "hide"; + PPTSld.Bobj.visibility = "hide"; + PPTSld.Eobj.visibility = "hide"; + } + return true; +} + +function overMe() { + this.bgColor = "blue"; +} + +function outMe() { + this.bgColor = "#AAAAAA"; +} + +function makeElement( whichEl, whichContainer ) { + if ( arguments.length == 1 ) { + whichContainer = PPTSld; + } + tmp = new Layer(100,whichContainer); + eval( whichEl + " = tmp" ); + return eval(whichEl); +} + +function initMe( obj, clr, text ) { + obj.bgColor = clr; +// obj.document.write("<a href='javascript:return false'>" + text + "</a>"); + obj.document.write( "<font size=2 face=Arial " ); + if ( !M_HasPrevSld() && (obj == PPTSld.Bobj ) ) { + obj.document.write( " color='#808080' " ); + } + else { + obj.onmouseover = overMe; + obj.onmouseout = outMe; + } + obj.document.write( " >   " + text +"</font> <layer top=0 left=0 width=100 height=40 ></layer>"); + obj.document.close(); + obj.captureEvents(Event.CLICK); + obj.color = "black"; +} + +function createCM() { + if ( base.IsFullScrMode() ) { + var clr = "#AAAAAA"; + PPTSld.shadeUobj = makeElement("SHADEU"); + PPTSld.shadeDobj = makeElement("SHADED"); + PPTSld.panelobj = makeElement("PANEL"); + PPTSld.stripUobj = makeElement("STRIPU"); + PPTSld.stripDobj = makeElement("STRIPD"); + PPTSld.shadeUobj.bgColor = "#BBBBBB"; + PPTSld.shadeDobj.bgColor = "#888888"; + PPTSld.stripUobj.bgColor = "#777777"; + PPTSld.stripDobj.bgColor = "#CCCCCC"; + PPTSld.panelobj.bgColor = clr; + PPTSld.Fobj = makeElement("Next"); + PPTSld.Bobj = makeElement("Previous"); + PPTSld.Eobj = makeElement("EndShow"); + initMe( PPTSld.Fobj, clr, "Next" ); + PPTSld.Fobj.onclick = M_GoNextSld; + + initMe( PPTSld.Bobj, clr, "Previous" ); + PPTSld.Bobj.onclick = M_GoPrevSld; + + initMe( PPTSld.Eobj, clr, "End Show"); + PPTSld.Eobj.onclick = base.CloseFullScreen; + } +} + +function IsContextMenu() { + return (g_ctxmenu == 1) +} +var g_notesTable = new Array() +var g_hiddenSlide = new Array() +makeSlide( 0,1,1); +makeSlide( 1,1,1); +makeSlide( 2,1,1); +makeSlide( 3,1,1); +makeSlide( 4,1,1); +makeSlide( 5,1,1); +makeSlide( 6,1,1); +makeSlide( 7,1,1); +makeSlide( 8,1,1); +makeSlide( 9,1,1); +makeSlide( 10,1,1); +makeSlide( 11,1,1); +makeSlide( 12,1,1); +makeSlide( 13,1,1); +makeSlide( 14,1,1); +makeSlide( 15,1,1); +makeSlide( 16,1,1); +makeSlide( 17,1,1); +makeSlide( 18,1,1); +makeSlide( 19,1,1); +makeSlide( 20,1,1); +makeSlide( 21,1,1); +makeSlide( 22,1,1); +makeSlide( 23,1,1); +makeSlide( 24,1,1); +makeSlide( 25,1,1); +makeSlide( 26,1,1); +makeSlide( 27,1,1); +makeSlide( 28,1,1); +makeSlide( 29,1,1); +makeSlide( 30,1,1); +makeSlide( 31,1,1); + +var END_SHOW_HREF = "endshow.htm", + OUTLINE_EXPAND_HREF = "outline_expanded.htm", + OUTLINE_COLLAPSE_HREF = "outline_collapsed.htm", + OUTLINE_NAVBAR_HREF = "outline_navigation_bar.htm", + NAVBAR_HREF = "navigation_bar.htm", + BLANK_NOTES_HREF = "blank_notes.htm", + NUM_VISIBLE_SLIDES = 32, + SIMPLE_FRAMESET = 0, + SLIDE_FRAME = "PPTSld", + NOTES_FRAME = "PPTNts", + OUTLINE_FRAME = "PPTOtl", + OUTLINE_NAVBAR_FRAME = "PPTOtlNav", + NAVBAR_FRAME = "PPTNav", + MAIN_FRAME = "MainFrame", + FS_NAVBAR_HREF = "fs_navigation_bar.htm", + isIEFiles = 2, + isNAVFiles = 8, + isFLATFiles = 16, + includeNotes = 1, + PPTPRESENTATION = 1; +var INITSLIDENUM = 1; + +var EndSlideShow = 0; +var g_outline_href = OUTLINE_COLLAPSE_HREF; +var g_fullscrMode = 0; +var FSWin = null; +var gtmpstr = document.location.href; +var g_baseURL = gtmpstr.substr(0, gtmpstr.lastIndexOf("/") ) + "/" + "WebQTLDemo_files"; +var g_showoutline = 1; +var g_shownotes = includeNotes; +var g_currentSlide = INITSLIDENUM, g_prevSlide = INITSLIDENUM; +var saveFSSlideNum = saveTPSlideNum = g_currentSlide; +var saveFSprevSlide = saveTPprevSlide = g_prevSlide; +var g_slideType="ie"; +var appVer = navigator.appVersion; +var msie = appVer.indexOf( "MSIE " ) + appVer.indexOf( "Internet Explorer " ); +var isnav = ( navigator.appName.indexOf( "Netscape" ) >= 0 ); +var msieWin31 = (appVer.indexOf( "Windows 3.1" ) > 0); +var ver = 0; +var g_done = 0; +var g_prevotlobjidx = 0; +var g_ShowFSDefault = 0; +var g_lastVisibleSld = 1; +var g_allHidden = false; +function IsIE() { + return (msie >= 0 ); +} + +function IsNav() { + return (isnav); +} +var msiePos = appVer.indexOf( "MSIE " ); +var inexPos = appVer.indexOf( "Internet Explorer " ); +if ( msiePos >= 0 ) + ver = parseFloat( appVer.substring( msiePos+5, appVer.indexOf ( ";", msiePos ) ) ); +else if( inexPos >= 0 ) + ver=parseFloat( appVer.substring( inexPos+18, appVer.indexOf(";",inexPos) ) ) +else + ver = parseInt( appVer ); + +//var g_supportsPPTHTML = 0; //!msieWin31 && ( ( msie >= 0 && ver >= 3.02 ) || ( msie < 0 && ver >= 3 ) ); + +function GetCurrentSlideNum() +{ + obj = GetHrefObj( g_currentSlide ); + if ( GetHrefObj( g_currentSlide ).m_origVisibility == 1 ) + return obj.m_slideIdx; + else + return g_currentSlide; +} + +function GetNumSlides() +{ + if ( GetHrefObj( g_currentSlide ).m_origVisibility == 1 ) + return NUM_VISIBLE_SLIDES; + else + return g_docTable.length; +} + +function GetHrefObj( slideIdx ) +{ return g_docTable[slideIdx - 1]; +} + +function GetSlideNum( slideHref ) +{ + for (ii=0; ii<g_docTable.length; ii++) { + if ( g_docTable[ii].m_slideHref == slideHref ) + return ii+1; + } + return 1; +} + +function GoToNextSld() +{ + targetIdx = g_currentSlide + 1; + if ( GetHrefObj( targetIdx-1 ).m_origVisibility == 0 ) { + if ( targetIdx<=g_docTable.length ) { + obj = GetHrefObj( targetIdx ); + obj.m_visibility = 1; + GoToSld( obj.m_slideHref ); + } + } + else { + obj = GetHrefObj( targetIdx ); + while ( obj && ( obj.m_origVisibility == 0 ) && ( targetIdx<=g_docTable.length ) ) + obj = GetHrefObj( targetIdx++ ); + if( obj && obj.m_origVisibility ) + GoToSld( obj.m_slideHref ); + } +} + +function GoToPrevSld() +{ + targetIdx = g_currentSlide - 1; + if ( targetIdx > 0 ) { + obj = GetHrefObj( targetIdx ); + while ( ( obj.m_visibility == 0 ) && ( targetIdx>0 ) ) + obj = GetHrefObj( targetIdx-- ); + GoToSld( obj.m_slideHref ); + } +} + +function GoToLast() +{ + targetIdx = g_docTable.length; + if ( targetIdx != g_currentSlide ) + GoToSld( GetHrefObj( targetIdx ).m_slideHref ); +} + +function GoToFirst() +{ GoToSld( GetHrefObj(1).m_slideHref ); +} + +function highlite() { + if ( IsFullScrMode() ) + return; + index = GetCurrentSlideNum(); + if ( !frames[MAIN_FRAME].frames[OUTLINE_FRAME] ) + return; + if ( msie < 0 ) { + if ( g_prevotlobjidx != 0 ) { + eval( "otlobj = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.LAYERID" + g_prevotlobjidx ); + otlobj.hidden = true; + } + else + index = GetCurrentSlideNum(); + eval( "otlobj = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.LAYERID" + index ); + otlobj.hidden = false; + + g_prevotlobjidx = index; + + return; + } + if ( !g_showoutline ) + return; + + backclr = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.body.bgColor; + textclr = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.body.text; + if ( g_prevotlobjidx != 0 ) { + eval( "otlobj = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.all.p" + g_prevotlobjidx ); + otlobj.style.backgroundColor = backclr; + otlobj.style.color = textclr; + otlobj.all.AREF.style.color = textclr; + } + else + index = GetCurrentSlideNum(); + eval( "otlobj = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.all.p" + index ); + otlobj.style.backgroundColor = textclr; + otlobj.style.color = backclr; + otlobj.all.AREF.style.color = backclr; + g_prevotlobjidx = index; +} + +function ChangeFrame( frame, href ) +{ +if ( IsFramesMode() ) { + if ( NAVBAR_FRAME == frame || OUTLINE_NAVBAR_FRAME == frame ) { + frames[frame].location.replace(href); + } + else if( ! ( ( OUTLINE_FRAME == frame && !g_showoutline) || (NOTES_FRAME == frame && !g_shownotes ) ) ){ + frames[MAIN_FRAME].frames[frame].location.href = href; + } + } + else { + if ( frame == NAVBAR_FRAME || frame == SLIDE_FRAME ) { + if( frame == NAVBAR_FRAME ) { + href = FS_NAVBAR_HREF; + + } + if( frame == NAVBAR_FRAME ) + window.frames[frame].location.replace(href); + else + window.frames[frame].location.href = href; + } + } + +} + +function shutEventPropagation() { + if ( IsNav() ) + return; + + var slideFrame; + if ( IsFramesMode() ) + slideFrame = frames[MAIN_FRAME].frames[SLIDE_FRAME]; + else + slideFrame = window.frames[SLIDE_FRAME]; + if ( slideFrame.event ) + slideFrame.event.cancelBubble=true; +} + +function GoToSld( slideHref ) +{ + shutEventPropagation(); + if ( slideHref != GetHrefObj( g_currentSlide ).m_slideHref || g_slideType != GetHrefObj( g_currentSlide ).type) { + g_prevSlide = g_currentSlide; + g_currentSlide = GetSlideNum( slideHref ); + g_slideType = GetHrefObj( g_currentSlide ).type; + obj = GetHrefObj( g_currentSlide ); + obj.m_visibility = 1; + ChangeFrame( SLIDE_FRAME, slideHref ); + if( !SIMPLE_FRAMESET ) + ChangeFrame( NOTES_FRAME, obj.m_notesHref ); + ChangeFrame( NAVBAR_FRAME, NAVBAR_HREF ); + + } +} + +function PrevSldViewed() +{ GoToSld( GetHrefObj( g_prevSlide ).m_slideHref ); +} + +function NoHref() {} + +function ExpandOutline( ) +{ + g_outline_href = OUTLINE_EXPAND_HREF; + ChangeFrame( OUTLINE_FRAME, OUTLINE_EXPAND_HREF ); + frames[OUTLINE_NAVBAR_FRAME].location.replace( OUTLINE_NAVBAR_HREF); +} + +function CollapseOutline() +{ + g_outline_href = OUTLINE_COLLAPSE_HREF; + ChangeFrame( OUTLINE_FRAME, OUTLINE_COLLAPSE_HREF ); + frames[OUTLINE_NAVBAR_FRAME].location.replace( OUTLINE_NAVBAR_HREF); + } + +function SlideUpdated( id ) +{ + if ( id != GetHrefObj( g_currentSlide ).m_slideHref ) { + g_prevSlide = g_currentSlide; + g_currentSlide = GetSlideNum( id ); + obj = GetHrefObj( g_currentSlide ); + if( !SIMPLE_FRAMESET ) + ChangeFrame( NOTES_FRAME, obj.m_notesHref ); + ChangeFrame( NAVBAR_FRAME, NAVBAR_HREF ); + } +} + +function hrefList( slideHref, notesHref, visible, slideIdx, type ) +{ + this.m_slideHref = slideHref; + this.m_notesHref = notesHref; + this.m_navbarHref = NAVBAR_HREF; + this.m_origVisibility = visible; + this.m_visibility = visible; + this.m_slideIdx = slideIdx; + this.type = type; +} + +function IsFullScrMode() { + return g_fullscrMode; +} + + +function IsFramesMode() { + return (1 - g_fullscrMode); +} + +function SldUpdated( id ) +{ + if ( ( id != GetHrefObj( g_currentSlide ).m_slideHref ) || ( g_currentSlide == g_lastVisibleSld ) ){ + g_prevSlide = g_currentSlide; + g_currentSlide = GetSlideNum( id ); + obj = GetHrefObj( g_currentSlide ); + if( !SIMPLE_FRAMESET ) + ChangeFrame( NOTES_FRAME, obj.m_notesHref ); + ChangeFrame( NAVBAR_FRAME, NAVBAR_HREF ); + } +} + +function ToggleOutline() { + g_showoutline = 1 - g_showoutline; + writeMyFrame(); +} + +function ShowHideNotes() { + g_shownotes = 1 - g_shownotes; + writeMyFrame(); +} + +function writeMyFrame() { + SetFSMode(0); + obj = frames[MAIN_FRAME]; + + var curslide = g_baseURL + "/" + GetHrefObj( g_currentSlide ).m_slideHref; + var curnotes = g_baseURL + "/" + GetHrefObj( g_currentSlide ).m_notesHref; + var otlhref = g_baseURL + "/" + g_outline_href; + if ( msie < 0 ) { + if ( ! g_showoutline && g_shownotes ) { + obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \ + <frameset rows=\"*,20%\" id=\"frameset2\" > \ + <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \ + <frame src=\"' + curnotes + '\" name=PPTNts marginheight=0 marginwidth=0> \ + </frameset> </html>' ); + } + else if( g_showoutline && g_shownotes ){ + obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \ + <frameset cols=\"20%,*\" id=\"frameset1\"> \ + <frame src=\"' + otlhref + '\" name=PPTOtl> \ + <frameset rows=\"*,20%\" id=\"frameset2\" > \ + <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \ + <frame src=\"' + curnotes + '\" name=PPTNts marginheight=0 marginwidth=0> \ + </frameset> </frameset></html>' ); + } + else if ( !g_shownotes && !g_showoutline ) { + obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \ + <frameset rows="*,0" frameborder=0 > \ + <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \ + </frameset> </html>' ); + } + else if( !g_shownotes && g_showoutline ) { + obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \ + <frameset cols=\"20%,*\" id=\"frameset1\"> \ + <frame src=\"' + otlhref + '\" name=PPTOtl> \ + <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \ + </frameset></html>' ); + } + obj.document.close(); + } + else { + if ( g_showoutline ) { + obj.PPTHorizAdjust.cols = "20%,*"; + obj.PPTOtl.location.reload(); + } + else { + obj.PPTHorizAdjust.cols = "0,*"; + } + if ( g_shownotes ) { + obj.PPTVertAdjust.rows = "*,20%"; + obj.PPTNts.location.href = curnotes; + } + else { + obj.PPTVertAdjust.rows = "*,0"; + } + } + ChangeFrame( OUTLINE_NAVBAR_FRAME, OUTLINE_NAVBAR_HREF ); +} + +function FullScreen() { + g_done = 0; + + + SetFSMode(1); + if ( msie >= 0 ) + FSWin = window.open( g_baseURL + "/" + "fullscreen.htm", null, "fullscreen=yes"); + else { + var height = screen.availHeight; + if ( window.navigator.platform.indexOf( "Mac" ) >= 0 ) { + height -= 30; + } + FSWin = window.open( g_baseURL + "/" + "fullscreen.htm", "null", "height="+ height + ",width=" + screen.availWidth + ",screenX=0,screenY=0"); + } +} + +function SetFSMode( i ) { + +} + +function Slide( i ) { + SetFSMode(0); + GoToSld(GetHrefObj(i).m_slideHref); +} + +function TP_GoToNextSld() { + SetFSMode(0); + GoToNextSld(); +} + +function TP_GoToPrevSld() { + SetFSMode(0); + GoToPrevSld(); +} + +function CloseFullScreen() { + g_done = 0; + + if ( IsNav() ){ + if ( self.opener ) + opener.FSWin = null; + } + window.close(); +} + +function slidenum(i) { + var slidename = "slide"; + if ( i < 10 ) + return ( slidename + "000" + i); + else if ( i < 100 ) + return ( slidename + "00" + i ); + else if ( i < 1000 ) + return (slidename + "0" + i ); + else + return (slidename + i ); +} +function UpdateLastVisibleSlide( index ) { + if ( g_lastVisibleSld < index ) + g_lastVisibleSld = index; +} + +function jpegArray( numSlides ) { +count_hidden = 0; + g_docTable = new Array(); + for( i=0; i<numSlides; i++ ) { + j = 2 * numSlides + i + 1; + var str = slidenum( j ) +".htm"; + if( g_notesTable[i] == 1 ) + g_docTable[i] = new hrefList( str, slidenum(i+1 ) + "_notes_pane.htm", g_hiddenSlide[i], i+1-count_hidden, "jpeg" ); + else + g_docTable[i] = new hrefList( str, BLANK_NOTES_HREF, g_hiddenSlide[i], i+1-count_hidden, "jpeg" ); + if ( !g_hiddenSlide[i] ) count_hidden++; + else UpdateLastVisibleSlide( i+1 ); + } +} + +function ieArray( numSlides ) { +count_hidden = 0; + g_docTable = new Array(); + for( i=0; i<numSlides; i++ ) { + var str = slidenum(i+1) +".htm"; + if( g_notesTable[i] == 1 ) + g_docTable[i] = new hrefList( str, slidenum( i+1 ) + "_notes_pane.htm", g_hiddenSlide[i], i+1-count_hidden, "ie" ); + else + g_docTable[i] = new hrefList( str, BLANK_NOTES_HREF, g_hiddenSlide[i], i+1-count_hidden, "ie" ); + if ( !g_hiddenSlide[i] ) count_hidden++; + else UpdateLastVisibleSlide( i+1 ); + } +} + +function navArray( numSlides ) { +count_hidden = 0; + g_docTable = new Array(); + for( i=0; i<numSlides; i++ ) { + j = numSlides + i + 1; + var str = slidenum( j ) +".htm"; + if( g_notesTable[i] == 1 ) + g_docTable[i] = new hrefList( str, slidenum(i+1 ) + "_notes_pane.htm", g_hiddenSlide[i], i+1-count_hidden, "nav" ); + else + g_docTable[i] = new hrefList( str, BLANK_NOTES_HREF, g_hiddenSlide[i], i+1-count_hidden, "nav" ); + if ( !g_hiddenSlide[i] ) count_hidden++; + else UpdateLastVisibleSlide( i+1 ); + } +} + +function LoadHTMLVersion() { + var os = window.navigator.platform.indexOf("Mac"); + if ( (msie || isnav ) && ( (os < 0 && ver >= 4 ) || ( os >= 0 && ver >= 5 ) || (os >=0 && msie < 0 && ver >= 4 ) ) ){ + if ( msie >= 0 ) { + if ( isIEFiles > 0 ) + ieArray( 32 ); + else if ( isFLATFiles > 0 ){ + /*if ( IsFramesMode() ) + StatusPlay("This presentation is optimized for use with older versions of your browser. Since you are using a more recent version of Microsoft Internet Explorer or Netscape Navigator, consider optimizing this presentation to take advantage of your current version's advanced capabilities."); */ + jpegArray( 32 ); + } + else + window.location.replace( "WebQTLDemo_files/error.htm" ); + } + else { + if ( isNAVFiles > 0 && ver < 5) + navArray( 32 ); + else if ( isFLATFiles > 0 ) { + /* if ( IsFramesMode() ) + StatusPlay("This presentation is optimized for use with older versions of your browser. Since you are using a more recent version of Microsoft Internet Explorer or Netscape Navigator, consider optimizing this presentation to take advantage of your current version's advanced capabilities."); */ + jpegArray( 32 ); + } + else + window.location.replace( "WebQTLDemo_files/error.htm" ); + } +} +else { + /* + if ( IsFramesMode() && !isWebTV() ) + StatusPlay("This presentation contains content that your browser may not be able to show properly. This presentation was optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator."); + */ + if ( isFLATFiles <= 0 ) { + /* if ( IsFramesMode() ) + window.alert("This presentation contains content that your browser may not be able to display properly. This presentation is optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator." ); + */ + window.location.replace( "WebQTLDemo_files/error.htm" ); + } + /* + else if ( IsFramesMode() && !isWebTV() ) + StatusPlay( "This presentation contains content that your browser may not be able to show properly. This presentation was optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator." ); + */ + jpegArray ( 32 ); + } + +} + +function isWebTV() { + if ( window.navigator.appName.indexOf( 'WebTV' ) >= 0 ) + return true; + return false; +} + +var count; +var statusText; +var statusfirst = 0; + function display50( text ) +{ + len = text.length; + if ( len < 50 && count < 2) { + window.status = text; + window.setTimeout( "repeat()", 300 ); + } + else { + var period = 200; + window.status = text; + newtext = text.substring( 1, len ); + if ( statusfirst ) { + statusfirst = 0; + period = 2000; + } + window.setTimeout( "display50( newtext )", period ); + } +} +function repeat( ) { + count++; + statusfirst = 1; + display50( statusText ); +} + +function StatusPlay( text ) { + count = 0; + statusText = text; + repeat( ); + } +function makeSlide( i, notes, visible ) { + g_notesTable[i] = notes; + g_hiddenSlide[i] = visible; +} + diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0001.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0001.htm new file mode 100755 index 00000000..4c783452 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0001.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: WebQTL Demonstration One please link to www.webqtl.org/search.html"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0001.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:6.89%;left:3.31%;width:96.42%;height:19.61%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";mso-margin-left-alt:232; mso-text-indent-alt:0;position:absolute;top:0%;left:1.09%;width:97.39%; height:100.0%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size:68%'><i>WebQTL Demonstration One<br> </i></span></span><span style='position:absolute;top:33.33%;left:4.23%;width:95.76%'><span style='font-size:68%'><i>please link to <br> </i></span></span><span style='position:absolute;top:58.55%;left:4.23%;width:95.76%'><span style='font-size:86%'><i>www.webqtl.org/search.html</i></span><span style='font-size:68%;mso-special-format:lastCR;display:none'><i><br> </i></span></span></div> </div> <div style='position:absolute;top:31.62%;left:5.43%;width:73.24%;height:45.05%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='position:absolute;top:0%;left:2.71%;width:97.28%; height:93.33%'> <div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:0%;left:0%;width:89.77%;height:39.91%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='mso-special-format: nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size: 99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part 1: How to discover shared </span></span><span style='position:absolute; top:30.52%;left:7.86%;width:86.54%'><span style='font-size:94%;color:#E9EB5D; mso-color-index:3'>expression patterns (slides </span></span><span style='position:absolute;top:61.05%;left:7.86%;width:86.54%'><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>2Ð14)<br> </span></span></div> <div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:48.31%;left:0%;width:84.94%;height:27.73%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='mso-special-format: nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size: 99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part 2. Discovering upstream </span></span><span style='position:absolute; top:43.93%;left:8.31%;width:91.46%'><span style='font-size:94%;color:#E9EB5D; mso-color-index:3'>modulators (15Ð25)<br> </span></span></div> <div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:84.45%;left:0%;width:100.0%;height:15.54%'><span style='position:absolute;top:0%;left:7.06%;width:92.93%'><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'><span style='mso-special-format: "numbullet3\,3";color:#FBFDB8;position:absolute;left:-7.6%;font-family:Times; font-size:99%'>3.</span></span><span style='font-size:94%;color:#E9EB5D; mso-color-index:3'>Discovering downstream targets</span></span></div> </div> </div> <img border=0 src="slide0001_image001.gif" style='position:absolute;top:21.9%; left:74.56%;width:23.57%;height:64.31%'> <div class=O style='position:absolute;top:79.32%;left:75.89%;width:10.46%; height:14.48%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:42.68%'><span style='font-family:"Arial Rounded MT Bold";font-size:233%;color:#6E6E6E'>RNA</span><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; display:none'><br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:46.34%;left:0%;width:82.27%;height:54.87%'><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; mso-special-format:lastCR;display:none'><br> </span></div> </div> <div class=O style='position:absolute;top:76.5%;left:4.37%;width:78.67%; height:13.07%'><span style='position:absolute;top:0%;left:0%;width:98.98%'><span style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D;mso-color-index: 3'><i>PowerPoint ÒNormal viewÓ has notes that </i></span></span><span style='position:absolute;top:51.35%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D;mso-color-index: 3'><i>may be useful companions to these slides.</i></span><span style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D;mso-color-index: 3;mso-special-format:lastCR;display:none'><br> </span></span></div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Welcome to a short demonstation of WebQTL. Please adjust the wize of windows on your monitor so that you can see part of this page as well as WebQTL windows. WebQTL will produce a potentially large number of new windows (pop-ups), so you may need to modify your browser preferences to permit pop-ups.<span style="mso-spacerun: yes"> </span>In this demonstration, we explore one important transcript expressed in the brain: the amyloid beta precursor protein messenger RNA. The product of this mRNA, the APP protein, is associated with Alzheimer disease.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>(Initial version of June 2003 by Rob Williams, Last edits June 16, 2003 by RW.)</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0001_image001.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0001_image001.gif new file mode 100755 index 00000000..5bcd338f --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0001_image001.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0001_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0001_notes_pane.htm new file mode 100755 index 00000000..0df634c1 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0001_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Welcome to a short demonstation of WebQTL. Please adjust the wize of windows on your monitor so that you can see part of this page as well as WebQTL windows. WebQTL will produce a potentially large number of new windows (pop-ups), so you may need to modify your browser preferences to permit pop-ups.<span style="mso-spacerun: yes"> </span>In this demonstration, we explore one important transcript expressed in the brain: the amyloid beta precursor protein messenger RNA. The product of this mRNA, the APP protein, is associated with Alzheimer disease.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>(Initial version of June 2003 by Rob Williams, Last edits June 16, 2003 by RW.)</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0002.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0002.htm new file mode 100755 index 00000000..2efd97f9 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0002.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0002.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:6.89%;left:2.78%;width:93.77%;height:14.66%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:0%;left:2.11%;width:96.46%;height:50.6%'><span style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts"; font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>or webqtl.org/search.html (mirror)</span></div> </div> <img border=0 src="slide0002_image002.gif" style='position:absolute;top:16.6%; left:2.51%;width:71.65%;height:81.27%'><img border=0 src="slide0002_image003.gif" style='position:absolute;top:49.82%;left:42.38%; width:20.39%;height:7.59%'><img border=0 src="slide0002_image004.gif" style='position:absolute;top:50.35%;left:62.78%;width:15.09%;height:36.74%'> <div class=O style='position:absolute;top:60.42%;left:79.33%;width:15.76%; height:11.48%'> <div style='position:absolute;top:0%;left:0%;width:100.0%;height:49.23%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>choose a<br> </span></div> <div style='position:absolute;top:50.76%;left:0%;width:96.63%;height:49.23%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>database</span></div> </div> <div class=O style='position:absolute;top:46.46%;left:79.33%;width:21.05%; height:11.48%'> <div style='position:absolute;top:0%;left:0%;width:89.93%;height:49.23%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>enter<br> </span></div> <div style='position:absolute;top:50.76%;left:0%;width:100.0%;height:49.23%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'><i>amyloid beta</i></span><span style='font-family:"Gill Sans";font-size: 250%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </div> <div class=O style='position:absolute;top:78.26%;left:79.73%;width:11.52%; height:11.48%'> <div style='position:absolute;top:0%;left:0%;width:89.65%;height:49.23%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>select<br> </span></div> <div style='position:absolute;top:50.76%;left:0%;width:100.0%;height:49.23%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>search</span></div> </div> <div style='position:absolute;top:.88%;left:3.31%;width:93.77%;height:9.36%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div style='position:absolute;top:0%;left:1.12%;width:97.45%;height:79.24%'> <div class=B1 style='mso-margin-left-alt:644;mso-text-indent-alt:420'></div> <div class=B2 style='mso-margin-left-alt:937;mso-text-indent-alt:716'></div> <div class=B3 style='mso-margin-left-alt:1232;mso-text-indent-alt:1009'></div> <div class=B4 style='mso-margin-left-alt:1544;mso-text-indent-alt:1304'></div> <div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 0;position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><span style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts"; font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>link to www.webqtl.org/search.html</span></div> </div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>WebQTL can be used to enter your own trait data or to work with data that we have entered for you.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Linking to http://www.webqtl.org/search.html will get you a version of the window above. It may not be identical in layout but it will have the key features. Please follow the intructions on the slide. Of course, we encourage you to enter your own terms of interest.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Two points: If you make a search term too complex you may get no hits. if you make it too simple (for example, APP) then you may get too much. Experiment.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>If you just link to</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>http://www.webqtl.org you will NOT see the window above but will see text that will help you to enter your own data.<span style="mso-spacerun: yes"> </span>To get to a version of the window shown above you will need to click on the phrase<span style="mso-spacerun: yes"> </span>RNA expression and Phenotype Databases in the upper banner.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>If you do not get a new page within 30 seconds then there is<span style="mso-spacerun: yes"> </span>a problem: try the mirror site http://webqtl.org/search.html.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0002_image002.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0002_image002.gif new file mode 100755 index 00000000..304daa18 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0002_image002.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0002_image003.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0002_image003.gif new file mode 100755 index 00000000..74f73adc --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0002_image003.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0002_image004.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0002_image004.gif new file mode 100755 index 00000000..1da7043d --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0002_image004.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0002_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0002_notes_pane.htm new file mode 100755 index 00000000..266bf3fb --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0002_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>WebQTL can be used to enter your own trait data or to work with data that we have entered for you.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Linking to http://www.webqtl.org/search.html will get you a version of the window above. It may not be identical in layout but it will have the key features. Please follow the intructions on the slide. Of course, we encourage you to enter your own terms of interest.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Two points: If you make a search term too complex you may get no hits. if you make it too simple (for example, APP) then you may get too much. Experiment.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>If you just link to</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>http://www.webqtl.org you will NOT see the window above but will see text that will help you to enter your own data.<span style="mso-spacerun: yes"> </span>To get to a version of the window shown above you will need to click on the phrase<span style="mso-spacerun: yes"> </span>RNA expression and Phenotype Databases in the upper banner.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>If you do not get a new page within 30 seconds then there is<span style="mso-spacerun: yes"> </span>a problem: try the mirror site http://webqtl.org/search.html.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0003.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0003.htm new file mode 100755 index 00000000..7e0f4be9 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0003.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Search results"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0003.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img border=0 src="slide0003_image005.gif" style='position:absolute;top:9.36%; left:9.13%;width:59.73%;height:87.45%'><img border=0 src="slide0003_image006.gif" style='position:absolute;top:72.26%;left:14.03%; width:62.51%;height:6.53%'> <div class=O style='position:absolute;top:68.37%;left:78.54%;width:21.05%; height:17.31%'> <div style='position:absolute;top:0%;left:0%;width:89.93%;height:32.65%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>highlight<br> </span></div> <div style='position:absolute;top:33.67%;left:0%;width:100.0%;height:32.65%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'><i>amyloid beta<br> </i></span></div> <div style='position:absolute;top:67.34%;left:0%;width:89.93%;height:32.65%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>then click</span><span style='font-family:"Gill Sans";font-size:250%; color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:-4.59%;left:7.81%;width:84.9%;height:18.55%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='position:absolute;top:24.76%;left:1.56%;width:96.87%; height:46.66%'><span style='font-size:91%'>Search results</span><span style='mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>If all goes well, you will see a version of this window. WebQTL will display up to about 100 hits. If a search generates larger numbers of hits then you will need to refine your search terms.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0003_image005.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0003_image005.gif new file mode 100755 index 00000000..5c7d29e8 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0003_image005.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0003_image006.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0003_image006.gif new file mode 100755 index 00000000..f75379b9 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0003_image006.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0003_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0003_notes_pane.htm new file mode 100755 index 00000000..5dbbbd2e --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0003_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>If all goes well, you will see a version of this window. WebQTL will display up to about 100 hits. If a search generates larger numbers of hits then you will need to refine your search terms.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0004.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0004.htm new file mode 100755 index 00000000..9980cf8b --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0004.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0004.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:1.41%;left:1.72%;width:97.61%;height:14.66%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:0%;left:2.03%;width:97.96%;height:50.6%'><span style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts"; font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>First page of data: The ÒTrait Data FormÓ</span></div> </div> <img border=0 src="slide0004_image007.gif" style='position:absolute;top:11.13%; left:3.31%;width:77.61%;height:86.39%'><img border=0 src="slide0004_image008.gif" style='position:absolute;top:56.0%;left:66.88%; width:14.7%;height:7.42%'> <div class=O style='position:absolute;top:50.7%;left:81.85%;width:20.0%; height:27.2%'> <div style='position:absolute;top:0%;left:0%;width:100.0%;height:20.12%'><span style='font-size:200%;color:#E9EB5D'><i>Click here<br> </i></span></div> <div style='position:absolute;top:19.48%;left:0%;width:83.44%;height:20.12%'><span style='font-size:200%;color:#E9EB5D'><i>to learn<br> </i></span></div> <div style='position:absolute;top:39.61%;left:0%;width:83.44%;height:20.12%'><span style='font-size:200%;color:#E9EB5D'><i>about<br> </i></span></div> <div style='position:absolute;top:59.09%;left:0%;width:83.44%;height:20.12%'><span style='font-size:200%;color:#E9EB5D'><i>data<br> </i></span></div> <div style='position:absolute;top:79.22%;left:0%;width:83.44%;height:20.12%'><span style='font-size:200%;color:#E9EB5D'><i>source</i></span></div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The Trait Data and Editing Form is the single more important page from the point of view of working with WebQTL data. Please read the text carefully. Explore the links, but do not close this page. We will need it many more times in this demonstration.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0004_image007.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0004_image007.gif new file mode 100755 index 00000000..db14d732 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0004_image007.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0004_image008.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0004_image008.gif new file mode 100755 index 00000000..8ac35a66 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0004_image008.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0004_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0004_notes_pane.htm new file mode 100755 index 00000000..22def119 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0004_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>The Trait Data and Editing Form is the single more important page from the point of view of working with WebQTL data. Please read the text carefully. Explore the links, but do not close this page. We will need it many more times in this demonstration.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0005.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0005.htm new file mode 100755 index 00000000..ab904a72 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0005.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0005.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:1.41%;left:3.31%;width:96.29%;height:14.66%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:0%;left:2.06%;width:97.93%;height:50.6%'><span style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts"; font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>Data sources: Phenotpyes and genotypes</span></div> </div> <img border=0 src="slide0005_image009.gif" style='position:absolute;top:10.77%; left:7.68%;width:84.5%;height:88.33%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>There are already five databases in WebQTL. Each will eventually have a page like this describing the data source and appropriate citations to these databases. The great majority of data in WebQTL were generated in our own labs and those of our collaborators.<span style="mso-spacerun: yes"> </span>We welcome you to use these data, but caution you that there are inevitably lots of little problems and issues that may compromise some results. Be cautious and skeptical. Ask us questions before you leap to publication. And please, if you find the data useful or can verify or refute data, LET US KNOW. We would like to add you to our reference section and add links to improvements.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0005_image009.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0005_image009.gif new file mode 100755 index 00000000..a6596e12 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0005_image009.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0005_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0005_notes_pane.htm new file mode 100755 index 00000000..916084ec --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0005_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>There are already five databases in WebQTL. Each will eventually have a page like this describing the data source and appropriate citations to these databases. The great majority of data in WebQTL were generated in our own labs and those of our collaborators.<span style="mso-spacerun: yes"> </span>We welcome you to use these data, but caution you that there are inevitably lots of little problems and issues that may compromise some results. Be cautious and skeptical. Ask us questions before you leap to publication. And please, if you find the data useful or can verify or refute data, LET US KNOW. We would like to add you to our reference section and add links to improvements.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0006.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0006.htm new file mode 100755 index 00000000..f3d4d1d5 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0006.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0006.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:1.06%;left:1.72%;width:47.94%;height:7.24%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:4.87%;left:4.14%;width:95.85%;height:78.04%'><span style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts"; font-size:99%'>l</span><span style='font-size:81%;color:#E9EB5D;mso-color-index: 3'>Return to Trait Data page </span></div> </div> <img border=0 src="slide0006_image010.gif" style='position:absolute;top:7.77%; left:.79%;width:48.47%;height:79.32%'><img border=0 src="slide0006_image011.gif" style='position:absolute;top:7.77%;left:50.46%;width:48.6%;height:78.79%'> <div style='position:absolute;top:1.06%;left:52.45%;width:43.84%;height:13.78%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:2.56%;left:4.53%;width:92.44%;height:41.02%'><span style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts"; font-size:99%'>l</span><span style='font-size:81%;color:#E9EB5D;mso-color-index: 3'>bottom of this page</span></div> </div> <div class=O style='position:absolute;top:86.39%;left:3.44%;width:109.13%; height:11.48%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>Trait data for each strain with SE when known. For array data </span></span><span style='position:absolute;top:50.76%;left:0%;width:99.02%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>the scale is ~ log base 2.<span style="mso-spacerun: yes"> </span></span><span style='font-size:183%;color:#E9EB5D;mso-color-index:3'>F1=13.752 = 2^13.752 = 13796 </span><span style='font-family:"Gill Sans";font-size:183%; color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;display:none'><br> </span></span></div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>This<span style="mso-spacerun: yes"> </span>slide shows you the<span style="mso-spacerun: yes"> </span>lower parts of the Trait Data Page. We expect to make many small modification of this page, so do not be surprised if some elements have been moved around.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0006_image010.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0006_image010.gif new file mode 100755 index 00000000..967e59ca --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0006_image010.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0006_image011.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0006_image011.gif new file mode 100755 index 00000000..1e1432cf --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0006_image011.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0006_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0006_notes_pane.htm new file mode 100755 index 00000000..be43575c --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0006_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>This<span style="mso-spacerun: yes"> </span>slide shows you the<span style="mso-spacerun: yes"> </span>lower parts of the Trait Data Page. We expect to make many small modification of this page, so do not be surprised if some elements have been moved around.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0007.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0007.htm new file mode 100755 index 00000000..052d2dcf --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0007.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0007.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:1.41%;left:3.31%;width:93.77%;height:14.66%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:0%;left:2.11%;width:97.45%;height:50.6%'><span style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts"; font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>Discovering shared expression patterns</span></div> </div> <img border=0 src="slide0007_image012.gif" style='position:absolute;top:16.6%; left:5.03%;width:86.22%;height:55.47%'><img border=0 src="slide0007_image013.gif" style='position:absolute;top:60.42%;left:45.82%; width:13.77%;height:14.84%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Finally, we can now start an analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>We ask a simple question:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Do differences in App transcript expression correlate with those of any other transcripts in the forebrain?</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0007_image012.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0007_image012.gif new file mode 100755 index 00000000..9cde2f15 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0007_image012.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0007_image013.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0007_image013.gif new file mode 100755 index 00000000..df9c9efb --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0007_image013.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0007_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0007_notes_pane.htm new file mode 100755 index 00000000..7d2536da --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0007_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Finally, we can now start an analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>We ask a simple question:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Do differences in App transcript expression correlate with those of any other transcripts in the forebrain?</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0008.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0008.htm new file mode 100755 index 00000000..7b1d488d --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0008.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0008.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:1.41%;left:3.31%;width:93.77%;height:14.66%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:0%;left:2.11%;width:96.46%;height:50.6%'><span style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts"; font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>The </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> transcript neighborhood</span></div> </div> <img border=0 src="slide0008_image014.gif" style='position:absolute;top:10.77%; left:5.82%;width:66.62%;height:88.33%'> <div class=O style='position:absolute;top:30.74%;left:75.23%;width:26.22%; height:18.72%'><span style='position:absolute;top:0%;left:0%;width:91.91%'><span style='font-size:150%;color:#E9EB5D;mso-color-index:3'><b>Question: </b></span><span style='font-size:133%;color:#E9EB5D;mso-color-index:3'><b>How </b></span></span><span style='position:absolute;top:21.69%;left:0%;width:97.47%'><span style='font-size:133%;color:#E9EB5D;mso-color-index:3'><b>many transcripts </b></span></span><span style='position:absolute;top:40.56%;left:0%;width:100.0%'><span style='font-size:133%;color:#E9EB5D;mso-color-index:3'><b>have correlations </b></span></span><span style='position:absolute;top:59.43%;left:0%;width:97.97%'><span style='font-size:133%;color:#E9EB5D;mso-color-index:3'><b>>0.7? What does </b></span></span><span style='position:absolute;top:79.24%;left:0%;width:85.35%'><span style='font-size:133%;color:#E9EB5D;mso-color-index:3'><b>this imply.</b></span></span></div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The answer is a strong Yes. A very large number of transcripts have correlations above 0.7 (absolute value) with App mRNA. The precise number today is 208. But this will change as we add more strains and arrays. In any case, this is a fairly large number and all of these correlations are significant at alpha .05 even when correcting for the enormous numbers<span style="mso-spacerun: yes"> </span>of tests (12422 tests).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>What does this imply?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>That there can be massive codependence of expression variance among transcripts. App is NOT an isolated instance. This is improtant biologically and statistically. From a statistical perspective, we would like to know how many ÒindependentÓ test we effectively are performing when we use array data in this way. Are we testing 12000 independent transcripts or just 1200 transcriptional ÒmodulesÓ each with blurred boarders but each with about 10 effective members. There is no answer yet, but we probaby have a large enough data set to begin to answer this question.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0008_image014.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0008_image014.gif new file mode 100755 index 00000000..d555e779 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0008_image014.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0008_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0008_notes_pane.htm new file mode 100755 index 00000000..5003f4a6 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0008_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>The answer is a strong Yes. A very large number of transcripts have correlations above 0.7 (absolute value) with App mRNA. The precise number today is 208. But this will change as we add more strains and arrays. In any case, this is a fairly large number and all of these correlations are significant at alpha .05 even when correcting for the enormous numbers<span style="mso-spacerun: yes"> </span>of tests (12422 tests).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>What does this imply?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>That there can be massive codependence of expression variance among transcripts. App is NOT an isolated instance. This is improtant biologically and statistically. From a statistical perspective, we would like to know how many ÒindependentÓ test we effectively are performing when we use array data in this way. Are we testing 12000 independent transcripts or just 1200 transcriptional ÒmodulesÓ each with blurred boarders but each with about 10 effective members. There is no answer yet, but we probaby have a large enough data set to begin to answer this question.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0009.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0009.htm new file mode 100755 index 00000000..82b93d4f --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0009.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0009.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:2.47%;left:6.62%;width:94.17%;height:14.66%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:0%;left:2.1%;width:98.03%;height:50.6%'><span style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts"; font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>Handdrawn sketch of the neighborhood</span></div> </div> <img border=0 src="slide0009_image015.gif" style='position:absolute;top:13.07%; left:9.53%;width:80.79%;height:80.38%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Many of the data types in the previous slide are hot-linked and it is easy to generate a small web of correlations between any transcript of interest and many other transcripts. In this case, we have used green lines between transcripts that have positive correlations, and red lines between transcripts that have negative correlations. Correlations have been multiplied by 100. The correlation of 0.96 between App and Hsp84-1 reads 96.<span style="mso-spacerun: yes"> </span>These are Pearson product moment correlations and they are sensitive to outliers. If you prefer, you can recompute Spearman rank order correlations.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Where did Ndr4 (lower left) come from? It is not in the list in the previous slide. Actually it is. Nomenclature changes rapidly. If you click on R74996 in the previous slide (the active webqtl version) you will see that it now has a new symbol and name.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>What are all of the<span style="mso-spacerun: yes"> </span>conventions in this correlation network sketch.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Times size=3>1.</font><font face=Helvetica size=3>The official gene symbol = App</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. OUr estimate of the location of these gene in the Mouse Genome Sequencing Consoritum version 3 build (MGSCv3). Chromosome followed by the megabase position relative to the centromere. (Mice only have one chromosome arm so this is an unambiguous coordinate. )</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. The pair of numbers: top is the highest expression among the strain set. The lower number is the lowest expression of that transcript among the strain set.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>4. Vertical number on the right side of each box: this is the probe set ID given by Affymetrix. We have truncated these probe set IDs so you will not see the usual<span style="mso-spacerun: yes"> </span>ÒatÓ. A single gene may be represented by more than 10 probe sets. Thus this ID number is essential to identify the actual data source.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>5. Lower right corner: a two digit number followed by plus and minus signs. These numbers are the correlation value (absolute value) of the 100th best correlated transcript. The plus and minus signs indicate the mean polarity of the correlations.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>6. The set of numbers that read 2@140* etc. These are the approximate locations of additive effect QTLs detected by WebQTL that we will describe in other slides. Read this as: App has a suggestive QTL on Chr 2 at about 140 Mb and the D allele inherited from DBA/2J confirms a higher expression level at this marker.<span style="mso-spacerun: yes"> </span>If there is no star symbol, then it is not even formally ÒsuggestiveÓ but does make an interesting looking blip on the QTL radar screen.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0009_image015.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0009_image015.gif new file mode 100755 index 00000000..4e9f96be --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0009_image015.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0009_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0009_notes_pane.htm new file mode 100755 index 00000000..bdcc6cd9 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0009_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Many of the data types in the previous slide are hot-linked and it is easy to generate a small web of correlations between any transcript of interest and many other transcripts. In this case, we have used green lines between transcripts that have positive correlations, and red lines between transcripts that have negative correlations. Correlations have been multiplied by 100. The correlation of 0.96 between App and Hsp84-1 reads 96.<span style="mso-spacerun: yes"> </span>These are Pearson product moment correlations and they are sensitive to outliers. If you prefer, you can recompute Spearman rank order correlations.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Where did Ndr4 (lower left) come from? It is not in the list in the previous slide. Actually it is. Nomenclature changes rapidly. If you click on R74996 in the previous slide (the active webqtl version) you will see that it now has a new symbol and name.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>What are all of the<span style="mso-spacerun: yes"> </span>conventions in this correlation network sketch.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Times size=2>1.</font><font face=Helvetica size=2>The official gene symbol = App</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. OUr estimate of the location of these gene in the Mouse Genome Sequencing Consoritum version 3 build (MGSCv3). Chromosome followed by the megabase position relative to the centromere. (Mice only have one chromosome arm so this is an unambiguous coordinate. )</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>3. The pair of numbers: top is the highest expression among the strain set. The lower number is the lowest expression of that transcript among the strain set.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>4. Vertical number on the right side of each box: this is the probe set ID given by Affymetrix. We have truncated these probe set IDs so you will not see the usual<span style="mso-spacerun: yes"> </span>ÒatÓ. A single gene may be represented by more than 10 probe sets. Thus this ID number is essential to identify the actual data source.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>5. Lower right corner: a two digit number followed by plus and minus signs. These numbers are the correlation value (absolute value) of the 100th best correlated transcript. The plus and minus signs indicate the mean polarity of the correlations.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>6. The set of numbers that read 2@140* etc. These are the approximate locations of additive effect QTLs detected by WebQTL that we will describe in other slides. Read this as: App has a suggestive QTL on Chr 2 at about 140 Mb and the D allele inherited from DBA/2J confirms a higher expression level at this marker.<span style="mso-spacerun: yes"> </span>If there is no star symbol, then it is not even formally ÒsuggestiveÓ but does make an interesting looking blip on the QTL radar screen.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0010.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0010.htm new file mode 100755 index 00000000..07768218 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0010.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0010.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:1.41%;left:3.31%;width:107.54%;height:14.66%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:0%;left:1.84%;width:98.15%;height:85.54%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='mso-special-format: nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size: 99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>What a network is likely to look like (but </span><span style='font-size:106%; color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%; color:#E9EB5D;mso-color-index:3'> </span></span><span style='position:absolute; top:39.43%;left:4.76%;width:80.92%'><span style='font-size:106%;color:#E9EB5D; mso-color-index:3'>will not be center of universe).</span></span></div> </div> <img border=0 src="slide0010_image016.gif" style='position:absolute;top:15.19%; left:6.35%;width:71.92%;height:82.5%'> <div class=O style='position:absolute;top:32.86%;left:45.82%;width:5.96%; height:3.71%'><span style='font-size:133%;color:#FF0F0F'><b><i>App</i></b></span></div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>What networks are likely to really look like. This slide is taken from Lumeta Inc.<span style="mso-spacerun: yes"> </span>(www.lumeta.com). It actually illustrates the structure of connections across the<span style="mso-spacerun: yes"> </span>Internet. The large green area is a major Internet provider (WorldCom before the fall?).<span style="mso-spacerun: yes"> </span>Check<span style="mso-spacerun: yes"> </span>out Lumeta to see some more lovely graphs of this sort. Most biologists are familiar with simple sketches, but this is what we will have to be prepared to contend with soon.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0010_image016.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0010_image016.gif new file mode 100755 index 00000000..6bec6eee --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0010_image016.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0010_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0010_notes_pane.htm new file mode 100755 index 00000000..2b497618 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0010_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>What networks are likely to really look like. This slide is taken from Lumeta Inc.<span style="mso-spacerun: yes"> </span>(www.lumeta.com). It actually illustrates the structure of connections across the<span style="mso-spacerun: yes"> </span>Internet. The large green area is a major Internet provider (WorldCom before the fall?).<span style="mso-spacerun: yes"> </span>Check<span style="mso-spacerun: yes"> </span>out Lumeta to see some more lovely graphs of this sort. Most biologists are familiar with simple sketches, but this is what we will have to be prepared to contend with soon.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0011.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0011.htm new file mode 100755 index 00000000..0da85156 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0011.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Are there experimental results to corroborate a link between App with Hsp84-1?"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0011.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:3.53%;left:2.11%;width:97.48%;height:21.02%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";mso-margin-left-alt:232; mso-text-indent-alt:0;position:absolute;top:18.48%;left:.95%;width:99.04%; height:61.34%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size:68%'><i>Are there experimental results to corroborate a link </i></span></span><span style='position:absolute;top:49.31%;left:4.25%;width:90.12%'><span style='font-size:68%'><i>between App with Hsp84-1?</i></span></span></div> </div> <div style='position:absolute;top:82.15%;left:4.1%;width:96.42%;height:18.55%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'></div> <div class=O style='position:absolute;top:29.5%;left:4.37%;width:99.33%; height:13.07%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D'><i>Yes: Heat shock 84-1 induces the expression of App, </i></span></span><span style='position: absolute;top:51.35%;left:0%;width:85.33%'><span style='font-family:"Gill Sans"; font-size:250%;color:#E9EB5D'><i>ubiquitin, and pyruvate kinase</i></span></span></div> <div class=O style='position:absolute;top:50.88%;left:5.16%;width:95.23%; height:19.78%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D'><i>Having ÒconfirmedÓ these known relations, we can </i></span></span><span style='position:absolute;top:33.92%;left:0%;width:99.72%'><span style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D'><i>now add new members to this family: Atp6l, Gnas, </i></span></span><span style='position: absolute;top:67.85%;left:0%;width:89.01%'><span style='font-family:"Gill Sans"; font-size:250%;color:#E9EB5D'><i>Ndr4. A thin veneer of functional genomics.</i></span></span></div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Having worked with WebQTL now for 30 minutes, do we know anything new? The hypothesis that we have generated (but not validated) is that three transcripts: Atp6l, Gnas, and Ndr4 are part of a family of genes that are coregulated in normal mouse forebrain with App and Hsp84-1. We need to add functional and mechanistic significance to this hypothesis to make it biologically vibrant. But from a statiistical standpoint it is a strong inference.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Please donÕt say: But these are mere correlations. A high correlation in this context has a biological basis. The real question is are we smart enough to understand the web (not chain) of causality that produced the correlation. Once we understand the web of causality, does it have utility? Very often the answer will be NO. This will often be the case when a high correlation is generated by linkage disequilibrium of sets of polymorphisms that modulate a set of mechanistically separated traits. Chromosomal linkage can produce correlations that are not mechanistic in the conventional sense used by molecular biologists. For example, clusters<span style="mso-spacerun: yes"> </span>of hox transcription factor genes tend to be close physically to keratin gene clusters, and one might expect shared patterns of variance produced by this linkage in a mapping panel, no matter how large.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>If Affymetrix designed probe sets with reasonable care, if we did the experiments correctly, if we sampled animals appropriately, then a correlation of 0.70 or higher between transcripts in the brain tells you that these two transcripts are effectively coupled in this set of animals under this set of conditions. More than 50% the variance in the expression of one transcript can be predicted from the other. That is a major piece of information that could be of significant clinical, economic, and predictive value, whatever its causes. Yes, correlation coefficients are noisy and have large error terms, but we have larger n of strains coming to the rescue. Expect more than 50 BXD lines soon.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>This is a thin veneer of functional genomics. It is enough to generate some marvelous hypotheses in a semi-automated way.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0011_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0011_notes_pane.htm new file mode 100755 index 00000000..214c9e08 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0011_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Having worked with WebQTL now for 30 minutes, do we know anything new? The hypothesis that we have generated (but not validated) is that three transcripts: Atp6l, Gnas, and Ndr4 are part of a family of genes that are coregulated in normal mouse forebrain with App and Hsp84-1. We need to add functional and mechanistic significance to this hypothesis to make it biologically vibrant. But from a statiistical standpoint it is a strong inference.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Please donÕt say: But these are mere correlations. A high correlation in this context has a biological basis. The real question is are we smart enough to understand the web (not chain) of causality that produced the correlation. Once we understand the web of causality, does it have utility? Very often the answer will be NO. This will often be the case when a high correlation is generated by linkage disequilibrium of sets of polymorphisms that modulate a set of mechanistically separated traits. Chromosomal linkage can produce correlations that are not mechanistic in the conventional sense used by molecular biologists. For example, clusters<span style="mso-spacerun: yes"> </span>of hox transcription factor genes tend to be close physically to keratin gene clusters, and one might expect shared patterns of variance produced by this linkage in a mapping panel, no matter how large.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>If Affymetrix designed probe sets with reasonable care, if we did the experiments correctly, if we sampled animals appropriately, then a correlation of 0.70 or higher between transcripts in the brain tells you that these two transcripts are effectively coupled in this set of animals under this set of conditions. More than 50% the variance in the expression of one transcript can be predicted from the other. That is a major piece of information that could be of significant clinical, economic, and predictive value, whatever its causes. Yes, correlation coefficients are noisy and have large error terms, but we have larger n of strains coming to the rescue. Expect more than 50 BXD lines soon.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>This is a thin veneer of functional genomics. It is enough to generate some marvelous hypotheses in a semi-automated way.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0012.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0012.htm new file mode 100755 index 00000000..3dae7024 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0012.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0012.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:1.41%;left:3.31%;width:105.43%;height:14.66%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:292;mso-text-indent-alt: 0;position:absolute;top:0%;left:1.0%;width:98.99%;height:50.6%'><span style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts"; font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>2.45 billion scatter plots: </span><span style='font-size:94%;color:#E9EB5D; mso-color-index:3'>here is one of the best</span></div> </div> <img border=0 src="slide0012_image017.gif" style='position:absolute;top:11.3%; left:6.62%;width:67.41%;height:82.68%'> <div class=O style='position:absolute;top:77.56%;left:41.19%;width:8.6%; height:7.42%'><span style='font-family:"Gill Sans";font-size:283%;color:#003399; mso-color-index:4'><i>App</i></span><span style='font-family:"Gill Sans"; font-size:283%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><i><br> </i></span></div> <img border=0 src="slide0012_image018.gif" alt="Text Box: Hsp84-1" style='position:absolute;top:36.04%;left:14.17%;width:6.88%;height:27.03%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The correlation between App and heat shock protein 84-1 transcript is most impressive.<span style="mso-spacerun: yes"> </span>Since WebQTL now contains total of about 70,000 traits in the BXD strains, we could produce as many as to 70k x 35k scatter plots of this type. Since all of the<span style="mso-spacerun: yes"> </span>correlations come for a common reference population, none<span style="mso-spacerun: yes"> </span>of the correlations are blantantly silly. However the great majority may be uninterpretable and a very large number may be meaningless given the signal-to-noise ratios of some measurements. With about 30 strains, correlations above 0.7 have a reasonably low false positive rate.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0012_image017.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0012_image017.gif new file mode 100755 index 00000000..e72a2bed --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0012_image017.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0012_image018.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0012_image018.gif new file mode 100755 index 00000000..7f4ca288 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0012_image018.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0012_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0012_notes_pane.htm new file mode 100755 index 00000000..0380a033 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0012_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>The correlation between App and heat shock protein 84-1 transcript is most impressive.<span style="mso-spacerun: yes"> </span>Since WebQTL now contains total of about 70,000 traits in the BXD strains, we could produce as many as to 70k x 35k scatter plots of this type. Since all of the<span style="mso-spacerun: yes"> </span>correlations come for a common reference population, none<span style="mso-spacerun: yes"> </span>of the correlations are blantantly silly. However the great majority may be uninterpretable and a very large number may be meaningless given the signal-to-noise ratios of some measurements. With about 30 strains, correlations above 0.7 have a reasonably low false positive rate.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0013.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0013.htm new file mode 100755 index 00000000..223f93fb --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0013.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0013.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:1.41%;left:3.31%;width:93.77%;height:14.66%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:0%;left:2.11%;width:96.46%;height:50.6%'><span style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts"; font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>Cross-tissue type correlations</span></div> </div> <img border=0 src="slide0013_image019.gif" style='position:absolute;top:11.83%; left:4.1%;width:71.52%;height:46.64%'><img border=0 src="slide0013_image020.gif" style='position:absolute;top:60.95%;left:4.1%;width:89.93%;height:35.33%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>We can compare App expression inthe forebrain against transcript expression in hematopoietic stem cells. Some of these correlations are significant, but it may be difficult to discovery of shared genetic (linkage disequilibrium) or molecular processes that give rise to these correlation.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The GNF Hematopoietic stem cell data belong to Gerald de Haan (University of Groningen) and Michael Cooke (Genomics Institute of the Novartis Research Foundation).</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0013_image019.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0013_image019.gif new file mode 100755 index 00000000..06da89a2 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0013_image019.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0013_image020.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0013_image020.gif new file mode 100755 index 00000000..0f0c6e98 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0013_image020.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0013_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0013_notes_pane.htm new file mode 100755 index 00000000..642ca80b --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0013_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>We can compare App expression inthe forebrain against transcript expression in hematopoietic stem cells. Some of these correlations are significant, but it may be difficult to discovery of shared genetic (linkage disequilibrium) or molecular processes that give rise to these correlation.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>The GNF Hematopoietic stem cell data belong to Gerald de Haan (University of Groningen) and Michael Cooke (Genomics Institute of the Novartis Research Foundation).</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0014.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0014.htm new file mode 100755 index 00000000..c0c82256 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0014.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0014.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:1.41%;left:3.31%;width:107.81%;height:14.66%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:0%;left:1.84%;width:98.15%;height:85.54%'><span style='position:absolute;top:0%;left:0%;width:99.37%'><span style='mso-special-format: nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size: 99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Cross-modal correlations: From mRNA to to </span></span><span style='position:absolute; top:39.43%;left:4.75%;width:95.24%'><span style='font-size:106%;color:#E9EB5D; mso-color-index:3'>anatomy and to behavior and pharmacology</span></span></div> </div> <img border=0 src="slide0014_image021.gif" style='position:absolute;top:15.37%; left:6.62%;width:53.37%;height:34.62%'><img border=0 src="slide0014_image022.gif" style='position:absolute;top:46.81%;left:17.35%; width:65.16%;height:53.0%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Another example, but in this case we are generating correlations between variation in transcript levels with a database of approximately 430 published (and unpublished) phenotypes from BXD strains. Notice that the N of strains is variable (from 21 to 28 above). Rank order statistics is more appropriate when N is under 30.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The Published Phenotypes database was prepared by Elissa Chesler and Robert Williams from data extracted from the literature or sent to us for inclusion by our colleagues. We especially thank John Crabbe (Oregon HSU) and Byron Jones (Pennsylvania SU) for providing us with large pre-compiled data tables.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0014_image021.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0014_image021.gif new file mode 100755 index 00000000..554d9257 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0014_image021.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0014_image022.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0014_image022.gif new file mode 100755 index 00000000..6e967236 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0014_image022.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0014_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0014_notes_pane.htm new file mode 100755 index 00000000..4750bc2e --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0014_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Another example, but in this case we are generating correlations between variation in transcript levels with a database of approximately 430 published (and unpublished) phenotypes from BXD strains. Notice that the N of strains is variable (from 21 to 28 above). Rank order statistics is more appropriate when N is under 30.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>The Published Phenotypes database was prepared by Elissa Chesler and Robert Williams from data extracted from the literature or sent to us for inclusion by our colleagues. We especially thank John Crabbe (Oregon HSU) and Byron Jones (Pennsylvania SU) for providing us with large pre-compiled data tables.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0015.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0015.htm new file mode 100755 index 00000000..5e01bacc --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0015.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: WebQTL link to www.webqtl.org/search.html"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0015.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:3.0%;left:2.11%;width:96.42%;height:19.61%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";mso-margin-left-alt:232; mso-text-indent-alt:0;position:absolute;top:0%;left:.96%;width:97.39%; height:100.0%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size:68%'><i>WebQTL<span style="mso-spacerun: yes"> </span><br> </i></span></span><span style='position: absolute;top:32.43%;left:4.37%;width:95.76%'><span style='font-size:68%'><i>link to <br> </i></span></span><span style='position:absolute;top:58.55%;left:4.37%; width:95.76%'><span style='font-size:86%'><i>www.webqtl.org/search.html</i></span><span style='font-size:68%;mso-special-format:lastCR;display:none'><i><br> </i></span></span></div> </div> <div style='position:absolute;top:36.57%;left:2.51%;width:73.24%;height:45.05%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='position:absolute;top:0%;left:2.71%;width:97.28%; height:81.96%'> <div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:0%;left:0%;width:94.6%;height:31.57%'><span style='position:absolute;top:0%;left:7.46%;width:92.53%'><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'><span style='mso-special-format: "numbullet3\,1";color:#FBFDB8;position:absolute;left:-8.06%;font-family:Times; font-size:99%'>1.</span></span><span style='font-size:94%;color:#E9EB5D; mso-color-index:3'>Discovering shared expression </span></span><span style='position:absolute;top:43.93%;left:7.46%;width:82.12%'><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>patterns<br> </span></span></div> <div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:41.14%;left:0%;width:84.94%;height:31.57%'><span style='position:absolute;top:0%;left:8.31%;width:91.46%'><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'><span style='mso-special-format: "numbullet3\,2";color:#FBFDB8;position:absolute;left:-9.09%;font-family:Times; font-size:99%'>2.</span></span><span style='font-size:94%;color:#E9EB5D; mso-color-index:3'>Discovering upstream </span></span><span style='position: absolute;top:43.93%;left:8.31%;width:91.46%'><span style='font-size:94%; color:#E9EB5D;mso-color-index:3'>modulators (QTLs)<br> </span></span></div> <div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:82.29%;left:0%;width:100.0%;height:17.7%'><span style='position:absolute;top:0%;left:7.06%;width:92.75%'><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'><span style='mso-special-format: "numbullet3\,3";color:#FBFDB8;position:absolute;left:-7.61%;font-family:Times; font-size:99%'>3.</span></span><span style='font-size:94%;color:#E9EB5D; mso-color-index:3'>Discovering downstream targets</span></span></div> </div> </div> <img border=0 src="slide0015_image023.gif" style='position:absolute;top:17.84%; left:74.17%;width:23.57%;height:64.31%'> <div class=O style='position:absolute;top:75.44%;left:74.56%;width:10.46%; height:14.48%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:42.68%'><span style='font-family:"Arial Rounded MT Bold";font-size:233%;color:#6E6E6E'>RNA</span><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; display:none'><br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:45.12%;left:0%;width:82.27%;height:54.87%'><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; mso-special-format:lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:82.15%;left:4.1%;width:96.42%;height:18.55%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'></div> <img border=0 src="slide0015_image024.gif" style='position:absolute;top:51.94%; left:47.28%;width:26.35%;height:10.77%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Part 2: Mapping upstream modulators or QTLs. A quantitative trait locus is a chromosomal region that harbors one or a few polymorphic gene loci that influence a trait. We are going to be looking for QTLs that modulate the steady state expression level of App in the adult mouse forebrain.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0015_image023.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0015_image023.gif new file mode 100755 index 00000000..5bcd338f --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0015_image023.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0015_image024.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0015_image024.gif new file mode 100755 index 00000000..550aeeb6 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0015_image024.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0015_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0015_notes_pane.htm new file mode 100755 index 00000000..e17d3a52 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0015_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Part 2: Mapping upstream modulators or QTLs. A quantitative trait locus is a chromosomal region that harbors one or a few polymorphic gene loci that influence a trait. We are going to be looking for QTLs that modulate the steady state expression level of App in the adult mouse forebrain.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0016.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0016.htm new file mode 100755 index 00000000..22b9419b --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0016.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <link rel=Stylesheet href="master05_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0016.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master05_background.gif" v:shapes="_x0000_s3075" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div class=O style='position:absolute;top:92.93%;left:8.74%;width:18.67%; height:5.83%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.48%'><span style='font-family:Times;font-size:117%;color:white;display:none'><br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.51%;left:0%;width:100.0%;height:48.48%'><span style='font-family:Times;font-size:117%;color:white;mso-special-format:lastCR; display:none'><br> </span></div> </div> <div class=O style='position:absolute;top:92.93%;left:35.49%;width:29.53%; height:5.83%'> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:48.48%'><span style='font-family:Times;font-size:117%;color:white; display:none'><br> </span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:51.51%;left:0%;width:100.0%; height:48.48%'><span style='font-family:Times;font-size:117%;color:white; mso-special-format:lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:2.12%;left:-2.64%;width:105.82%;height:11.13%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:0%;left:0%;width:100.0%;height:88.88%'> <div style='text-align:center;mso-line-spacing:"%0 0 0";mso-margin-left-alt: 16;mso-text-indent-alt:16;position:absolute;top:0%;left:0%;width:100.0%; height:67.85%'><span style='font-family:Arial;font-size:267%;color:#E9EB5D'><i>How to make recombinant inbred strains (RI)</i></span><span style='font-family: Arial;font-size:150%;color:aqua;display:none'><br> </span></div> <div style='text-align:center;mso-line-spacing:"%0 0 0";mso-margin-left-alt: 16;mso-text-indent-alt:16;position:absolute;top:60.71%;left:6.25%;width:87.48%; height:39.28%'><span style='font-family:Arial;font-size:150%;color:aqua; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <img border=0 src="slide0016_image025.gif" style='position:absolute;top:28.79%; left:45.43%;width:18.14%;height:1.06%'><img border=0 src="slide0016_image026.gif" style='position:absolute;top:20.31%;left:28.21%; width:1.98%;height:11.83%'> <div style='position:absolute;top:15.01%;left:25.03%;width:19.47%;height:10.07%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:8.77%;left:6.8%;width:93.19%; height:78.94%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>C57BL/6J (B)<br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:83.21%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <img border=0 src="slide0016_image027.gif" style='position:absolute;top:20.31%; left:30.46%;width:1.98%;height:11.83%'> <div style='position:absolute;top:15.01%;left:62.25%;width:16.55%;height:10.07%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:8.77%;left:8.0%;width:92.8%; height:78.94%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>DBA/2J (D)<br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:82.75%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <img border=0 src="slide0016_image028.gif" style='position:absolute;top:20.31%; left:66.62%;width:4.23%;height:11.83%'><img border=0 src="slide0016_image029.gif" style='position:absolute;top:35.51%;left:23.97%; width:50.86%;height:1.23%'><img border=0 src="slide0016_image030.gif" style='position:absolute;top:35.68%;left:24.1%;width:.66%;height:4.06%'><img border=0 src="slide0016_image031.gif" style='position:absolute;top:35.68%; left:40.92%;width:.52%;height:4.06%'><img border=0 src="slide0016_image032.gif" style='position:absolute;top:35.68%;left:57.61%;width:.52%;height:4.06%'><img border=0 src="slide0016_image033.gif" style='position:absolute;top:35.68%; left:74.3%;width:.52%;height:3.88%'> <div style='position:absolute;top:42.75%;left:5.69%;width:6.75%;height:12.72%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:8.33%;left:19.6%;width:70.58%; height:81.94%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:49.15%'><span style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F1<br> </b></span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:50.84%;left:0%;width:83.33%;height:49.15%'><span style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format:lastCR; display:none'><b><br> </b></span></div> </div> </div> <img border=0 src="slide0016_image034.gif" style='position:absolute;top:39.92%; left:22.25%;width:4.23%;height:11.83%'><img border=0 src="slide0016_image035.gif" style='position:absolute;top:39.92%;left:38.94%; width:4.23%;height:11.83%'><img border=0 src="slide0016_image036.gif" style='position:absolute;top:39.92%;left:55.62%;width:4.23%;height:11.83%'><img border=0 src="slide0016_image037.gif" style='position:absolute;top:39.39%; left:72.84%;width:4.23%;height:11.83%'><img border=0 src="slide0016_image038.gif" style='position:absolute;top:43.46%;left:43.97%; width:11.12%;height:3.53%'><img border=0 src="slide0016_image039.gif" style='position:absolute;top:60.95%;left:20.66%;width:9.8%;height:3.53%'> <div style='position:absolute;top:71.73%;left:58.41%;width:20.52%;height:27.03%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:12.41%;left:6.45%;width:87.09%; height:82.35%'> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:69.84%'><span style='position:absolute;top:0%;left:0%;width:99.25%'><span style='font-family:Arial;font-size:117%;color:#FFFF99'><b>20 generations </b></span></span><span style='position:absolute;top:39.77%;left:0%;width:100.0%'><span style='font-family:Arial;font-size:117%;color:#FFFF99'><b>brother-sister </b></span></span><span style='position:absolute;top:80.68%;left:0%;width:100.0%'><span style='font-family:Arial;font-size:117%;color:#FFFF99'><b>matings</b></span><span style='font-family:Arial;font-size:233%;color:#FFFF99;display:none'><b><br> </b></span></span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:73.8%;left:0%;width:100.0%; height:26.98%'><span style='font-family:Arial;font-size:233%;color:#FFFF99; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> </div> <img border=0 src="slide0016_image040.gif" style='position:absolute;top:60.95%; left:50.72%;width:9.93%;height:3.53%'><img border=0 src="slide0016_image041.gif" style='position:absolute;top:62.72%;left:54.03%;width:4.37%;height:28.97%'><img border=0 src="slide0016_image042.gif" style='position:absolute;top:61.13%; left:79.86%;width:10.86%;height:3.53%'><img border=0 src="slide0016_image043.gif" style='position:absolute;top:62.36%;left:83.97%; width:4.1%;height:28.79%'> <div style='position:absolute;top:92.93%;left:21.72%;width:9.4%;height:10.07%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:8.77%;left:12.67%;width:84.5%; height:78.94%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD1</span><span style='font-family:Arial;font-size:150%;color:#484848;display:none'><br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:83.33%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#484848;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:92.75%;left:51.78%;width:9.4%;height:10.07%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:8.77%;left:12.67%;width:84.5%; height:78.94%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD2<br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:83.33%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:92.93%;left:80.79%;width:10.99%;height:6.0%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:14.7%;left:12.04%;width:87.95%; height:64.7%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD80</span></div> </div> <div style='position:absolute;top:90.45%;left:64.1%;width:17.74%;height:17.84%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:5.94%;left:7.46%;width:92.53%; height:87.12%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.86%'><span style='font-family:Arial;font-size:300%;color:#FFFF99'>+ É +<br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:50.0%;left:0%;width:83.87%;height:48.86%'><span style='font-family:Arial;font-size:300%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:62.89%;left:4.9%;width:6.75%;height:12.72%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:6.94%;left:19.6%;width:70.58%; height:81.94%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:49.15%'><span style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F2<br> </b></span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:50.84%;left:0%;width:83.33%;height:49.15%'><span style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format:lastCR; display:none'><b><br> </b></span></div> </div> </div> <img border=0 src="slide0016_image044.gif" style='position:absolute;top:54.24%; left:18.01%;width:75.62%;height:1.06%'><img border=0 src="slide0016_image045.gif" style='position:absolute;top:54.06%;left:17.88%; width:.66%;height:3.88%'><img border=0 src="slide0016_image046.gif" style='position:absolute;top:54.24%;left:32.45%;width:.52%;height:3.88%'><img border=0 src="slide0016_image047.gif" style='position:absolute;top:54.24%; left:48.07%;width:.52%;height:4.06%'><img border=0 src="slide0016_image048.gif" style='position:absolute;top:54.24%;left:62.78%;width:.52%;height:4.06%'><img border=0 src="slide0016_image049.gif" style='position:absolute;top:54.24%; left:77.74%;width:.52%;height:4.06%'><img border=0 src="slide0016_image050.gif" style='position:absolute;top:54.59%;left:92.71%;width:.52%;height:3.71%'><img border=0 src="slide0016_image051.gif" style='position:absolute;top:44.87%; left:49.13%;width:.79%;height:10.07%'><img border=0 src="slide0016_image052.gif" style='position:absolute;top:57.59%;left:15.89%;width:4.23%;height:11.83%'><img border=0 src="slide0016_image053.gif" style='position:absolute;top:57.59%; left:30.86%;width:4.37%;height:11.83%'><img border=0 src="slide0016_image054.gif" style='position:absolute;top:57.59%;left:46.35%; width:4.23%;height:11.83%'><img border=0 src="slide0016_image055.gif" style='position:absolute;top:57.59%;left:60.92%;width:4.23%;height:11.83%'><img border=0 src="slide0016_image056.gif" style='position:absolute;top:57.59%; left:75.62%;width:4.23%;height:11.83%'><img border=0 src="slide0016_image057.gif" style='position:absolute;top:57.59%;left:90.86%; width:4.23%;height:11.83%'><img border=0 src="slide0016_image058.gif" style='position:absolute;top:84.09%;left:56.42%;width:1.98%;height:1.41%'><img border=0 src="slide0016_image059.gif" style='position:absolute;top:80.21%; left:25.96%;width:1.98%;height:11.83%'><img border=0 src="slide0016_image060.gif" style='position:absolute;top:84.98%;left:86.09%; width:1.85%;height:2.12%'> <div style='position:absolute;top:75.61%;left:1.58%;width:14.17%;height:14.13%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:7.5%;left:.93%;width:97.19%; height:83.75%'> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:7.69%;width:83.65%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'><b>BXD RI<br> </b></span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:32.83%;left:0%;width:100.0%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'><b>Strain set<br> </b></span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:67.16%;left:7.69%;width:83.65%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> </div> <img border=0 src="slide0016_image061.gif" style='position:absolute;top:12.36%; left:14.17%;width:10.59%;height:6.36%'><img border=0 src="slide0016_image062.gif" style='position:absolute;top:10.6%;left:76.42%; width:14.3%;height:8.3%'> <div style='position:absolute;top:20.84%;left:17.48%;width:9.8%;height:14.13%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:7.5%;left:6.75%;width:86.48%; height:83.75%'> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:7.81%;width:82.81%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>fully<br> </span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:32.83%;left:0%;width:100.0%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>inbred<br> </span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:67.16%;left:7.81%;width:82.81%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:38.16%;left:2.91%;width:12.05%;height:10.07%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:8.77%;left:3.29%;width:92.3%; height:78.94%'> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>isogenic<br> </span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:51.11%;left:8.33%;width:83.33%; height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:54.41%;left:1.85%;width:12.45%;height:14.13%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:7.5%;left:2.12%;width:93.61%; height:83.75%'> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:7.95%;width:82.95%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>hetero-<br> </span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:32.83%;left:0%;width:100.0%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>geneous<br> </span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:67.16%;left:7.95%;width:82.95%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:74.91%;left:29.0%;width:22.25%;height:22.08%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:4.0%;left:5.35%;width:88.09%; height:90.4%'> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:79.64%'><span style='position:absolute;top:0%;left:.67%;width:99.32%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>Recombined </span></span><span style='position:absolute;top:25.55%;left:.67%;width:99.32%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>chromosomes </span></span><span style='position:absolute;top:51.11%;left:0%;width:100.0%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>are needed for </span></span><span style='position:absolute;top:75.55%;left:.67%;width:99.32%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>mapping<br> </span></span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:80.53%;left:.67%;width:99.32%; height:19.46%'><span style='font-family:Arial;font-size:150%;color:#FFFF99; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:10.24%;left:25.56%;width:10.46%;height:10.07%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:8.77%;left:12.65%;width:87.34%; height:78.94%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>female<br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:84.05%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:10.24%;left:64.5%;width:8.21%;height:10.07%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:8.77%;left:14.51%;width:80.64%; height:78.94%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>male<br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:84.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:30.56%;left:78.01%;width:19.47%;height:10.07%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:15.78%;left:6.12%;width:93.19%; height:71.92%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:41.46%'><span style='font-family:Arial;font-size:117%;color:#FFFF99'>chromosome pair</span><span style='font-family:Arial;font-size:150%;color:#FFFF99;display:none'><br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:46.34%;left:0%;width:83.21%;height:53.65%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <img border=0 src="slide0016_image063.gif" style='position:absolute;top:31.09%; left:65.82%;width:12.84%;height:2.82%'> <div style='position:absolute;top:86.21%;left:3.97%;width:10.06%;height:14.48%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:4.87%;left:5.26%;width:86.84%; height:85.36%'> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:9.09%;width:83.33%; height:24.28%'><span style='font-family:Arial;font-size:117%;color:#E9EB5D'>Inbred<br> </span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:25.71%;left:0%;width:100.0%; height:24.28%'><span style='font-family:Arial;font-size:117%;color:#E9EB5D'>Isogenic<br> </span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:50.0%;left:6.06%;width:90.9%; height:24.28%'><span style='font-family:Arial;font-size:117%;color:#E9EB5D'>siblings</span><span style='font-family:Arial;font-size:117%;color:aqua;display:none'><br> </span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:75.71%;left:9.09%;width:83.33%; height:24.28%'><span style='font-family:Arial;font-size:117%;color:aqua; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <img border=0 src="slide0016_image064.gif" style='position:absolute;top:79.32%; left:83.7%;width:1.98%;height:11.83%'><img border=0 src="slide0016_image065.gif" style='position:absolute;top:79.85%;left:53.5%;width:1.98%;height:11.83%'><img border=0 src="slide0016_image066.gif" style='position:absolute;top:80.21%; left:23.44%;width:1.98%;height:11.83%'> <div style='position:absolute;top:18.72%;left:43.04%;width:13.77%;height:9.89%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:10.71%;left:9.61%;width:90.38%;height:76.78%'><span style='font-family:Arial;font-size:300%;color:aqua'>B</span><span style='font-family:Arial;font-size:300%;color:#FFFF99'>X</span><span style='font-family:Arial;font-size:300%;color:#FF1911'>D</span></div> </div> <img border=0 src="slide0016_image067.gif" style='position:absolute;top:27.2%; left:32.98%;width:31.39%;height:4.06%'><img border=0 src="slide0016_image068.gif" style='position:absolute;top:66.25%;left:60.92%; width:1.98%;height:3.18%'><img border=0 src="slide0016_image069.gif" style='position:absolute;top:64.31%;left:15.89%;width:1.98%;height:5.3%'><img border=0 src="slide0016_image070.gif" style='position:absolute;top:57.59%; left:75.62%;width:1.98%;height:5.65%'><img border=0 src="slide0016_image071.gif" style='position:absolute;top:28.44%;left:48.87%;width:.92%;height:8.12%'><img border=0 src="slide0016_image072.gif" style='position:absolute;top:62.19%; left:23.84%;width:3.57%;height:16.96%'><img border=0 src="slide0016_image073.gif" style='position:absolute;top:61.48%;left:63.17%; width:1.98%;height:8.12%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The next set of slides provide a very short interlude on QTL mapping. You will need to do some independent reading on this topic if this is your first exposure to QTL mapping. The recombinant inbred strains that we are using in WebQTL and in this particular demo were generated about 25 years ago by Dr. Ben Taylor at The Jackson Laboratory. He crossed a female C57BL/6J mouse with a male DBA/2J mice. At the bottom of this slide we have schematized one chromosome pair from three out of 80 BXD RI strains.<span style="mso-spacerun: yes"> </span>The dashed vertical lines that lead to the final BXD RI lines involve 20 full sib matings (about 6 years of breeding). Some lines die<span style="mso-spacerun: yes"> </span>out during inbreeding. For example, there is no extant BXD3 or BXD4 strain.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0016_image025.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0016_image025.gif new file mode 100755 index 00000000..8d9c9c1c --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0016_image025.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0016_image026.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0016_image026.gif new file mode 100755 index 00000000..dbd66f42 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0016_image026.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0016_image027.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0016_image027.gif new file mode 100755 index 00000000..dbd66f42 --- /dev/null +++ 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name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The next set of slides provide a very short interlude on QTL mapping. You will need to do some independent reading on this topic if this is your first exposure to QTL mapping. The recombinant inbred strains that we are using in WebQTL and in this particular demo were generated about 25 years ago by Dr. Ben Taylor at The Jackson Laboratory. He crossed a female C57BL/6J mouse with a male DBA/2J mice. At the bottom of this slide we have schematized one chromosome pair from three out of 80 BXD RI strains.<span style="mso-spacerun: yes"> </span>The dashed vertical lines that lead to the final BXD RI lines involve 20 full sib matings (about 6 years of breeding). Some lines die<span style="mso-spacerun: yes"> </span>out during inbreeding. For example, there is no extant BXD3 or BXD4 strain.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0017.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0017.htm new file mode 100755 index 00000000..1b5ac952 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0017.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0017.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img border=0 src="slide0017_image074.gif" style='position:absolute;top:40.45%; left:73.24%;width:14.56%;height:5.3%'> <div class=O style='position:absolute;top:40.81%;left:74.56%;width:11.92%; height:7.24%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:60.97%'><span style='font-family:Gadget;font-size:150%;color:white'>aa<br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:41.46%;left:0%;width:100.0%;height:60.97%'><span style='font-family:Gadget;font-size:150%;color:white;mso-special-format:lastCR; display:none'><br> </span></div> </div> <img border=0 src="slide0017_image075.gif" style='position:absolute;top:16.6%; left:73.24%;width:14.56%;height:5.3%'> <div class=O style='position:absolute;top:16.96%;left:74.56%;width:11.92%; height:7.24%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:60.97%'><span style='font-family:Gadget;font-size:150%;color:white'>aaaa<br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:41.46%;left:0%;width:100.0%;height:60.97%'><span style='font-family:Gadget;font-size:150%;color:white;mso-special-format:lastCR; display:none'><br> </span></div> </div> <div style='position:absolute;top:20.31%;left:71.65%;width:25.96%;height:19.78%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:9.82%;left:5.1%;width:95.4%; height:83.03%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:45.16%'><span style='font-size:267%;color:#E2EBF0'>D2 strain</span><span style='font-family: Palatino;font-size:333%;color:#FBFDB8;display:none'><br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:49.46%;left:0%;width:88.77%;height:50.53%'><span style='font-family:Palatino;font-size:333%;color:#FBFDB8;mso-special-format: lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:43.81%;left:71.65%;width:25.56%;height:19.78%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:10.71%;left:5.18%;width:94.81%; height:83.03%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:45.16%'><span style='font-size:267%;color:#F6BF69'>B6 strain</span><span style='font-family: Palatino;font-size:333%;color:#F6BF69;display:none'><br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:48.38%;left:0%;width:87.43%;height:50.53%'><span style='font-family:Palatino;font-size:333%;color:#F6BF69;mso-special-format: lastCR;display:none'><br> </span></div> </div> </div> <img border=0 src="slide0017_image076.gif" style='position:absolute;top:17.31%; left:31.25%;width:1.32%;height:42.22%'><img border=0 src="slide0017_image077.gif" style='position:absolute;top:40.63%;left:31.39%; width:39.86%;height:3.53%'> <div style='position:absolute;top:17.13%;left:40.0%;width:30.59%;height:31.44%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:11.23%;left:4.32%;width:90.9%; height:83.7%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:61.74%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size: 233%;color:#E9EB5D'><i>amount of </i></span></span><span style='position:absolute; top:59.78%;left:0%;width:100.0%'><span style='font-size:233%;color:#E9EB5D'><i>transcript</i></span><span style='font-family:Palatino;font-size:367%;color:#E9EB5D;display:none'><br> </span></span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:65.77%;left:0%;width:100.0%;height:34.89%'><span style='font-family:Palatino;font-size:367%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:6.0%;left:72.45%;width:21.32%;height:19.78%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:9.82%;left:6.21%;width:87.57%; height:83.03%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:45.16%'><span style='font-size:267%;color:white'>4 </span><span style='font-size:233%; color:white'>units</span><span style='font-family:Palatino;font-size:333%; color:#E9EB5D;display:none'><br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:49.46%;left:0%;width:100.0%;height:50.53%'><span style='font-family:Palatino;font-size:333%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:29.5%;left:72.45%;width:21.32%;height:19.78%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:10.71%;left:6.21%;width:87.57%; height:83.03%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:45.16%'><span style='font-size:267%;color:white'>2</span><span style='font-size:233%; color:white'> units</span><span style='font-family:Palatino;font-size:333%; color:#E9EB5D;display:none'><br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:48.38%;left:0%;width:100.0%;height:50.53%'><span style='font-family:Palatino;font-size:333%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </div> </div> <img border=0 src="slide0017_image078.gif" style='position:absolute;top:15.72%; left:31.25%;width:40.26%;height:5.47%'> <div class=O style='position:absolute;top:17.84%;left:9.93%;width:4.76%; height:16.43%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#E2EBF0'>D<br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:49.46%;left:0%;width:83.33%;height:50.53%'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR;display:none'><br> </span></div> </div> <div class=O style='position:absolute;top:17.84%;left:17.88%;width:4.23%; height:16.43%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#F6BF69'>B<br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:49.46%;left:0%;width:84.37%;height:50.53%'><span style='font-size:300%;color:#F6BF69;mso-special-format:lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:77.73%;left:5.43%;width:104.37%;height:26.32%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='position:absolute;top:8.72%;left:1.26%;width:98.73%; height:87.24%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:62.3%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size: 233%;color:#E2EBF0'>D</span><span style='font-size:233%;color:#E9EB5D'> </span><span style='font-size:200%;color:#E9EB5D'>and </span><span style='font-size:233%; color:#F6BF69'>B</span><span style='font-size:233%;color:#E9EB5D'> </span><span style='font-size:200%;color:#E9EB5D'>may be SNP-like variants in the promoter </span></span><span style='position:absolute;top:61.72%;left:0%;width:97.55%'><span style='font-size:200%;color:#E9EB5D'>itself (cis QTL) or in </span><span style='font-size:200%;color:#EAEC5E'>upstream genes (trans QTLs)</span><span style='font-size:300%;color:#E9EB5D;display:none'><br> </span></span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:63.84%;left:0%;width:86.88%;height:36.15%'><span style='font-size:300%;color:#E9EB5D;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div class=O style='position:absolute;top:7.59%;left:4.23%;width:22.78%; height:16.25%'> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:0%;left:1.74%;width:97.09%; height:33.69%'><span style='font-size:200%;color:#E9EB5D'>UPSTREAM<br> </span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:32.6%;left:0%;width:100.0%; height:33.69%'><span style='font-size:200%;color:#E9EB5D'>modulators<br> </span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:66.3%;left:4.65%;width:90.69%; height:33.69%'><span style='font-size:200%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:7.59%;left:44.5%;width:17.21%;height:18.19%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:3.88%;left:6.92%;width:83.84%; height:90.29%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#E2EBF0'>High<br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:49.46%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:63.78%;left:8.74%;width:6.62%;height:18.19%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='position:absolute;top:3.88%;left:20.0%;width:72.0%; height:90.29%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#E2EBF0'>D<br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:49.46%;left:0%;width:83.33%;height:50.53%'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:63.78%;left:15.09%;width:6.22%;height:18.19%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='position:absolute;top:3.88%;left:19.14%;width:68.08%; height:90.29%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#F6BF69'>B<br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:49.46%;left:0%;width:84.37%;height:50.53%'><span style='font-size:300%;color:#F6BF69;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:71.02%;left:7.54%;width:16.02%;height:12.72%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='position:absolute;top:5.55%;left:7.43%;width:91.73%; height:86.11%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.0%'><span style='font-size:200%;color:#E9EB5D'><i>cis QTL</i></span><span style='font-size:200%;color:#E9EB5D;display:none'><br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:48.38%;left:0%;width:82.88%;height:50.0%'><span style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <img border=0 src="slide0017_image079.gif" style='position:absolute;top:57.24%; left:-1.05%;width:101.98%;height:7.59%'> <div class=O style='position:absolute;top:44.16%;left:47.15%;width:9.4%; height:12.72%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:51.38%'><span style='font-size:233%;color:#F6BF69'>Low<br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:50.0%;left:0%;width:83.09%;height:51.38%'><span style='font-size:233%;color:#F6BF69;mso-special-format:lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:58.12%;left:.79%;width:114.56%;height:6.53%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:10.81%;left:1.15%;width:98.84%;height:72.97%'><span style='font-family:Gadget;font-size:167%;color:white'>>>>>PROMOTER--ATG-Exon1-Intron1-Exon2-Intron2 - etc-3'UTR >>>>></span></div> </div> <img border=0 src="slide0017_image080.gif" style='position:absolute;top:37.98%; left:8.6%;width:13.77%;height:20.67%'> <div class=O style='position:absolute;top:39.75%;left:10.06%;width:3.57%; height:12.01%'> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white'><b><br> </b></span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:52.94%;left:7.4%;width:85.18%; height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> <div class=O style='position:absolute;top:40.1%;left:17.48%;width:3.57%; height:12.01%'> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white'><b><br> </b></span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:51.47%;left:7.4%;width:85.18%; height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> <img border=0 src="slide0017_image081.gif" style='position:absolute;top:33.74%; left:8.6%;width:13.77%;height:20.67%'> <div class=O style='position:absolute;top:35.86%;left:17.48%;width:3.57%; height:12.01%'> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white'><b><br> </b></span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:51.47%;left:7.4%;width:85.18%; height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> <div class=O style='position:absolute;top:35.51%;left:10.06%;width:3.57%; height:12.01%'> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white'><b><br> </b></span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:51.47%;left:7.4%;width:85.18%; height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> <div class=O style='position:absolute;top:37.8%;left:20.66%;width:.13%; height:12.01%'> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white; display:none'><b><br> </b></span></div> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:51.47%;left:0%;width:100.0%; height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> <img border=0 src="slide0017_image082.gif" style='position:absolute;top:27.38%; left:4.9%;width:21.45%;height:21.37%'> <div style='position:absolute;top:27.38%;left:5.03%;width:21.05%;height:12.72%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='position:absolute;top:5.55%;left:6.28%;width:93.71%; height:86.11%'> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.0%'><span style='font-size:200%;color:#E9EB5D'><i>trans QTL</i></span><span style='font-size:200%;color:#E9EB5D;display:none'><br> </span></div> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:48.38%;left:0%;width:83.22%;height:50.0%'><span style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>This slide is illustrates two categories of QTLs that modulate variability in transcript abundance.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. cis QTLs are defined as QTLs that are closely linked to the gene whose transcript is the measured trait. For example, a polymorphism in the promoter that affects the binding of a transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms in enhancers. They may also be polymorphisms in neigghboring genes.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. trans QTLs map far enough away from the location of the gene that gives rise to the transcript that is being measured so that we can be quite certain that the QTL is not IN the gene itself. The most blatant type of trans-QTL would be a polymorphism in a transcription factor. BUT in the majority of cases, the trans QTLs can be far removed in a mechanistic sense from the actual events modulating transcript abundance. That is why there are three overlappoing arrows above.<span style="mso-spacerun: yes"> </span>The way in which an upstream polymorphism influences a downstream difference in mRNA abundance can be very indirect. Effects can :</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>a.<span style="mso-spacerun: yes"> </span>cross tissue types (a polymorphic liver enzyme may affect CNS gene expression)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>b.<span style="mso-spacerun: yes"> </span>cross time (the modulator is only expressed for one day during development but has permanent effects in adults),</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>c.<span style="mso-spacerun: yes"> </span>may be contingent on environmental factors (heat shock may trigger the expression of a polymorphic factor that affects mRNA abundance).</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0017_image074.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image074.gif new file mode 100755 index 00000000..105788e5 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image074.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0017_image075.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image075.gif new file mode 100755 index 00000000..105788e5 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image075.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0017_image076.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image076.gif new file mode 100755 index 00000000..09cae4e5 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image076.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0017_image077.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image077.gif new file mode 100755 index 00000000..a22eaad4 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image077.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0017_image078.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image078.gif new file mode 100755 index 00000000..f2ccb116 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image078.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0017_image079.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image079.gif new file mode 100755 index 00000000..85ea98da --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image079.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0017_image080.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image080.gif new file mode 100755 index 00000000..ec80f547 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image080.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0017_image081.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image081.gif new file mode 100755 index 00000000..9ac1cef5 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image081.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0017_image082.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image082.gif new file mode 100755 index 00000000..bcf8004c --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0017_image082.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0017_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0017_notes_pane.htm new file mode 100755 index 00000000..a11a8b2a --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0017_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>This slide is illustrates two categories of QTLs that modulate variability in transcript abundance.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>1. cis QTLs are defined as QTLs that are closely linked to the gene whose transcript is the measured trait. For example, a polymorphism in the promoter that affects the binding of a transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms in enhancers. They may also be polymorphisms in neigghboring genes.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. trans QTLs map far enough away from the location of the gene that gives rise to the transcript that is being measured so that we can be quite certain that the QTL is not IN the gene itself. The most blatant type of trans-QTL would be a polymorphism in a transcription factor. BUT in the majority of cases, the trans QTLs can be far removed in a mechanistic sense from the actual events modulating transcript abundance. That is why there are three overlappoing arrows above.<span style="mso-spacerun: yes"> </span>The way in which an upstream polymorphism influences a downstream difference in mRNA abundance can be very indirect. Effects can :</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2><span style="mso-spacerun: yes"> </span>a.<span style="mso-spacerun: yes"> </span>cross tissue types (a polymorphic liver enzyme may affect CNS gene expression)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2><span style="mso-spacerun: yes"> </span>b.<span style="mso-spacerun: yes"> </span>cross time (the modulator is only expressed for one day during development but has permanent effects in adults),</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2><span style="mso-spacerun: yes"> </span>c.<span style="mso-spacerun: yes"> </span>may be contingent on environmental factors (heat shock may trigger the expression of a polymorphic factor that affects mRNA abundance).</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0018.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0018.htm new file mode 100755 index 00000000..552d31b1 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0018.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: WebQTL to exploring upstream control"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0018.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:2.29%;left:4.1%;width:105.16%;height:9.01%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";position:absolute;top:11.76%; left:1.25%;width:98.86%;height:82.35%'><span style='font-family:Verdana; font-size:73%'><i>WebQTL to exploring upstream control</i></span></div> </div> <img border=0 src="slide0018_image083.gif" style='position:absolute;top:13.07%; left:5.16%;width:89.66%;height:62.19%'><img border=0 src="slide0018_image084.gif" style='position:absolute;top:19.25%;left:55.49%; width:19.2%;height:25.97%'> <div class=O style='position:absolute;top:16.43%;left:74.3%;width:15.49%; height:5.65%'><span style='font-family:"Gill Sans";font-size:217%;color:#FF0F0F'>Just click</span></div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Back to the demo. Please bring the Traiit Data and Editing window to the front and look for the Interval Mapping button. Please confirm that you are back to the trait amyloid beta precursor protein.<span style="mso-spacerun: yes"> </span>If so, then just click the button.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notice that the default for:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Select Chrs (chromosomes) is ALL</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Select Probes is Probe Set</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Options: Permuation test YES<span style="mso-spacerun: yes"> </span>(1000 is the default number)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Options: Bootstrap test YES (1000 is the default number)</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0018_image083.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0018_image083.gif new file mode 100755 index 00000000..eb07999f --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0018_image083.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0018_image084.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0018_image084.gif new file mode 100755 index 00000000..32b75679 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0018_image084.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0018_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0018_notes_pane.htm new file mode 100755 index 00000000..50a3e6c2 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0018_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Back to the demo. Please bring the Traiit Data and Editing window to the front and look for the Interval Mapping button. Please confirm that you are back to the trait amyloid beta precursor protein.<span style="mso-spacerun: yes"> </span>If so, then just click the button.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Notice that the default for:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Select Chrs (chromosomes) is ALL</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Select Probes is Probe Set</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Options: Permuation test YES<span style="mso-spacerun: yes"> </span>(1000 is the default number)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Options: Bootstrap test YES (1000 is the default number)</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0019.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0019.htm new file mode 100755 index 00000000..9040b37a --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0019.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: WebQTL to exploring upstream control."> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0019.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:2.29%;left:4.1%;width:106.88%;height:9.01%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";mso-margin-left-alt:233; mso-text-indent-alt:0;position:absolute;top:11.76%;left:.99%;width:99.0%; height:82.35%'><span style='font-family:Verdana;font-size:73%'><i>WebQTL to exploring upstream control.</i></span></div> </div> <img border=0 src="slide0019_image085.gif" style='position:absolute;top:27.2%; left:1.72%;width:96.68%;height:51.76%'> <div class=O style='position:absolute;top:13.78%;left:19.33%;width:60.52%; height:6.53%'><span style='font-size:233%;color:#E9EB5D'><i>App maps on Chr 16 here</i></span></div> <img border=0 src="slide0019_image086.gif" style='position:absolute;top:15.9%; left:68.34%;width:14.43%;height:37.98%'><img border=0 src="slide0019_image087.gif" style='position:absolute;top:53.18%;left:13.5%; width:14.43%;height:37.98%'> <div class=O style='position:absolute;top:82.86%;left:26.88%;width:90.59%; height:14.48%'> <div style='position:absolute;top:0%;left:0%;width:83.33%;height:51.21%'><span style='font-size:267%;color:#E9EB5D'><i>Is App modulated by Chr 2?<br> </i></span></div> <div style='position:absolute;top:50.0%;left:0%;width:100.0%;height:51.21%'><span style='font-size:267%;color:#E9EB5D'><i>Probably, but donÕt bet the farm. </i></span></div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>This is the main output type: a so-called full genome interval map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The X-axis represents all 19 autosomes and the X chromosome as if they were laid end to end with short gaps between the telomere of one chromosome and the centromere of the next chromosome (mouse chromsomes only have a single long arm and the centromere represents the origin of each chromosome for numerical purpose: 0 centimorgans and almost 0 megabases). The blue labels along the bottom of the figure list a subset of markers that were used in mapping. We used 753 markers to perform the mapping but here we just list five markers per chromosome.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The thick blue wavy line running across chromsomes summarizes the strength of association between variation in the phenotype (App expression differences) and the two genotypes of 753 markers and the intervals between markers (hence, interval mapping).<span style="mso-spacerun: yes"> </span>The height of the wave (blue Y-axis to the left) provides the likelihood ratio statistic (LRS). Divide by 4.61 to convert these values to LOD scores.<span style="mso-spacerun: yes"> </span>Or you can read them as a chi-square-like statistic.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The red line and the red axis to the far right provides an estimate of the effect<span style="mso-spacerun: yes"> </span>that a QTL has on expression of App (this estimate of the addtive effect tends to be an overestimate). If the red line is below the X-axis then this means that the allele inherited from C57BL/6J (B6 or B) at a particular marker is associated with higher values. If the red line is above the X-axis then the DBA/2J allele (D2 or D) is associated with higher traits. Multiply the additive effect size by 2 to estimate the difference between the set of strains that have the B/B genotype and the D/D genotype at a specific marker. For example, on Chr 2 the red line<span style="mso-spacerun: yes"> </span>peaks at a value<span style="mso-spacerun: yes"> </span>of about 0.25. That means that this region of chromosome 2 is responsible for a 0.5 unit expression difference between B/B strains and the D/D strains. Since the units are log base 2, this is 2^0.5, or about a 41% difference in expression with the D/D group being high.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The yellow histogram bars: These summarize the results of a whole-genome bootstrap of the trait that is performed 1000 times. What is a bootstrap? A bootstrap provides you a metho of evaluating whether results are robust. If we drop out one strain, do we still get the same results? When mapping quantitative traits, each strain normally gets one equally weighted vote. But inthe bootstrap procedure, we give each strain a random weighting factor of between 0 and 1.<span style="mso-spacerun: yes"> </span>We then remap the trait and find THE SINGLE BEST LRS VALUE per bootstrap. We do this 1000 times. In this example, most bootstrap results cluster on Chr 2 under the LRS peak. That is somewhat reassuring. But notice that a substantial number of bootstrap results prefer Chr 7 or Chr 18.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The horizontal dashed lines at 9.6 and 15.9. These lines are the LRS values associated with the suggestive and significant false positive rates for genome-wide scans established by permuations of phenotypes across genotypes. We shuffle randomly 1000 times and obtain a distribution of peak LRS scores to generate a null distribution. Five percent of the time, one of these permuted data sets will have a peak LRS higher than 15.9. We call that level the 0.05 significance threshold for a whole genome scan. The p = 0.67 point is the the suggestive level, and corresponds to the green dashed line.<span style="mso-spacerun: yes"> </span>These thresholds are conservative for transcripts that have expression variation that is highly heritable. The putative or suggestive QTL on Chr 2 is probably more than just suggestive.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>One other point: the mapping procedure we use is computationally very fast, but it is relatively simple. We are not looking for gene-gene interactions and we are not fitting multiple QTLs in combinations.<span style="mso-spacerun: yes"> </span>Consider this QTL analysis a first pass that will highlight hot spots and warm spots that are worth following up on using more sophisticated models.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>CLICKABLE REGIONS:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. If you click on the Chromosome number then you will generate a new map just for that chromosome.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. If you click on the body of the map, say on the blue line, then you will generate a view<span style="mso-spacerun: yes"> </span>on a 10 Mb window of that part of the genome from the UCSC Genome Browser web site.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. If you click on a marker symbol, then you will generate a new Trait data and editing window with the genotypes loaded into the window just like any other trait. More on this later.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>NOTE: you can drag these maps off of the browser window and onto your desktop. The will be saved as PNG or PDF files. You can import them into Photoshop or other programs.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0019_image085.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0019_image085.gif new file mode 100755 index 00000000..03a2878d --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0019_image085.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0019_image086.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0019_image086.gif new file mode 100755 index 00000000..3327e4da --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0019_image086.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0019_image087.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0019_image087.gif new file mode 100755 index 00000000..227fce55 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0019_image087.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0019_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0019_notes_pane.htm new file mode 100755 index 00000000..cbe88cf0 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0019_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>This is the main output type: a so-called full genome interval map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The X-axis represents all 19 autosomes and the X chromosome as if they were laid end to end with short gaps between the telomere of one chromosome and the centromere of the next chromosome (mouse chromsomes only have a single long arm and the centromere represents the origin of each chromosome for numerical purpose: 0 centimorgans and almost 0 megabases). The blue labels along the bottom of the figure list a subset of markers that were used in mapping. We used 753 markers to perform the mapping but here we just list five markers per chromosome.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The thick blue wavy line running across chromsomes summarizes the strength of association between variation in the phenotype (App expression differences) and the two genotypes of 753 markers and the intervals between markers (hence, interval mapping).<span style="mso-spacerun: yes"> </span>The height of the wave (blue Y-axis to the left) provides the likelihood ratio statistic (LRS). Divide by 4.61 to convert these values to LOD scores.<span style="mso-spacerun: yes"> </span>Or you can read them as a chi-square-like statistic.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The red line and the red axis to the far right provides an estimate of the effect<span style="mso-spacerun: yes"> </span>that a QTL has on expression of App (this estimate of the addtive effect tends to be an overestimate). If the red line is below the X-axis then this means that the allele inherited from C57BL/6J (B6 or B) at a particular marker is associated with higher values. If the red line is above the X-axis then the DBA/2J allele (D2 or D) is associated with higher traits. Multiply the additive effect size by 2 to estimate the difference between the set of strains that have the B/B genotype and the D/D genotype at a specific marker. For example, on Chr 2 the red line<span style="mso-spacerun: yes"> </span>peaks at a value<span style="mso-spacerun: yes"> </span>of about 0.25. That means that this region of chromosome 2 is responsible for a 0.5 unit expression difference between B/B strains and the D/D strains. Since the units are log base 2, this is 2^0.5, or about a 41% difference in expression with the D/D group being high.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The yellow histogram bars: These summarize the results of a whole-genome bootstrap of the trait that is performed 1000 times. What is a bootstrap? A bootstrap provides you a metho of evaluating whether results are robust. If we drop out one strain, do we still get the same results? When mapping quantitative traits, each strain normally gets one equally weighted vote. But inthe bootstrap procedure, we give each strain a random weighting factor of between 0 and 1.<span style="mso-spacerun: yes"> </span>We then remap the trait and find THE SINGLE BEST LRS VALUE per bootstrap. We do this 1000 times. In this example, most bootstrap results cluster on Chr 2 under the LRS peak. That is somewhat reassuring. But notice that a substantial number of bootstrap results prefer Chr 7 or Chr 18.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The horizontal dashed lines at 9.6 and 15.9. These lines are the LRS values associated with the suggestive and significant false positive rates for genome-wide scans established by permuations of phenotypes across genotypes. We shuffle randomly 1000 times and obtain a distribution of peak LRS scores to generate a null distribution. Five percent of the time, one of these permuted data sets will have a peak LRS higher than 15.9. We call that level the 0.05 significance threshold for a whole genome scan. The p = 0.67 point is the the suggestive level, and corresponds to the green dashed line.<span style="mso-spacerun: yes"> </span>These thresholds are conservative for transcripts that have expression variation that is highly heritable. The putative or suggestive QTL on Chr 2 is probably more than just suggestive.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>One other point: the mapping procedure we use is computationally very fast, but it is relatively simple. We are not looking for gene-gene interactions and we are not fitting multiple QTLs in combinations.<span style="mso-spacerun: yes"> </span>Consider this QTL analysis a first pass that will highlight hot spots and warm spots that are worth following up on using more sophisticated models.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>CLICKABLE REGIONS:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>1. If you click on the Chromosome number then you will generate a new map just for that chromosome.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2. If you click on the body of the map, say on the blue line, then you will generate a view<span style="mso-spacerun: yes"> </span>on a 10 Mb window of that part of the genome from the UCSC Genome Browser web site.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>3. If you click on a marker symbol, then you will generate a new Trait data and editing window with the genotypes loaded into the window just like any other trait. More on this later.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>NOTE: you can drag these maps off of the browser window and onto your desktop. The will be saved as PNG or PDF files. You can import them into Photoshop or other programs.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0020.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0020.htm new file mode 100755 index 00000000..d21bef3e --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0020.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: The whole neighborhood is modulated!"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0020.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:2.29%;left:4.1%;width:105.82%;height:9.01%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";position:absolute;top:11.76%; left:1.25%;width:98.87%;height:82.35%'><span style='font-family:Verdana; font-size:73%'><i>The whole neighborhood is modulated!</i></span></div> </div> <img border=0 src="slide0020_image088.gif" style='position:absolute;top:13.07%; left:9.53%;width:80.79%;height:80.38%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>App has a suggestive QTL on Chr 2. What about the neighbors that we defined as having shared expression patterns. This figure shows that members of the immediate App neigborhood share a weak Chr 2 QTL.<span style="mso-spacerun: yes"> </span>That is what the blue oval in the background is meant to represent. But some transcripts, such as Ndr4 and Psen2 do not share this Chr 2 interval.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>QUESTION: What kind of headway can we make in detemining what polymorphism or polymorphisms on Chr 2 near 130 Mb might contribute to the variance in the expression of all of these important transcripts?</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0020_image088.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0020_image088.gif new file mode 100755 index 00000000..4e9f96be --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0020_image088.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0020_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0020_notes_pane.htm new file mode 100755 index 00000000..78ea1866 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0020_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>App has a suggestive QTL on Chr 2. What about the neighbors that we defined as having shared expression patterns. This figure shows that members of the immediate App neigborhood share a weak Chr 2 QTL.<span style="mso-spacerun: yes"> </span>That is what the blue oval in the background is meant to represent. But some transcripts, such as Ndr4 and Psen2 do not share this Chr 2 interval.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>QUESTION: What kind of headway can we make in detemining what polymorphism or polymorphisms on Chr 2 near 130 Mb might contribute to the variance in the expression of all of these important transcripts?</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0021.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0021.htm new file mode 100755 index 00000000..3d02bcf8 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0021.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Which gene is the QTL?"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0021.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:2.29%;left:4.1%;width:93.9%;height:9.01%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";position:absolute;top:11.76%; left:1.41%;width:97.03%;height:82.35%'><span style='font-family:Verdana; font-size:73%'><i>Which gene is the QTL?</i></span></div> </div> <img border=0 src="slide0021_image089.gif" style='position:absolute;top:13.07%; left:5.03%;width:58.27%;height:37.98%'><img border=0 src="slide0021_image090.gif" style='position:absolute;top:46.81%;left:3.31%; width:68.87%;height:51.94%'><img border=0 src="slide0021_image091.gif" style='position:absolute;top:38.51%;left:55.62%;width:24.76%;height:25.08%'> <div class=O style='position:absolute;top:7.77%;left:75.09%;width:21.05%; height:28.97%'> <div style='text-align:center;position:absolute;top:0%;left:8.17%;width:83.64%; height:25.6%'><span style='font-size:267%;color:#E9EB5D'><i>Right <br> </i></span></div> <div style='text-align:center;position:absolute;top:25.0%;left:0%;width:100.0%; height:25.6%'><span style='font-size:267%;color:#E9EB5D'><i>position<br> </i></span></div> <div style='text-align:center;position:absolute;top:50.0%;left:8.17%; width:83.64%;height:25.6%'><span style='font-size:267%;color:#E9EB5D'><i>&<br> </i></span></div> <div style='text-align:center;position:absolute;top:75.0%;left:8.17%; width:83.64%;height:25.6%'><span style='font-size:267%;color:#E9EB5D'><i>high r</i></span></div> </div> <div class=O style='position:absolute;top:50.7%;left:72.58%;width:28.87%; height:14.48%'> <div style='text-align:center;position:absolute;top:0%;left:8.71%;width:83.48%; height:51.21%'><span style='font-size:267%;color:#E9EB5D'><i>good<br> </i></span></div> <div style='text-align:center;position:absolute;top:50.0%;left:0%;width:100.0%; height:51.21%'><span style='font-size:267%;color:#E9EB5D'><i>candidates</i></span></div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4><b>Candidate Genes: </b><span style="mso-spacerun: yes"> </span>The best we can do at this point is to make an educated guess about the candidacy status of all genes in the QTL support interval. For sake of argument, lets say that we are confident that the polymorphism is located between 130 and 150 Mb (20 Mb, equivalent to roughly 10 cM). There will typically be 12 to 15 genes per Mb, so we now would like to evaluate 240 to 300 positional candidates. We would like to highlight the biologically relevant subset of candidates. We could look through gene ontologies and expression levels to help us winnow the list. An alternate way avaiable using WebQTL is to generate a list of those genes in this 20 Mb interval that have transcripts that co-vary in expression with App expression.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>To do this, go back to the Trait Data and Editing window. Sort the correlations by position. Select Return = 500. Then scroll down the list to see positional candidates that share expression with App.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>There are several candidates that have high correlation with App even in this short 20 Mb interval. We can rank them by correlation, but they are all close.<span style="mso-spacerun: yes"> </span>There is one other imporant approach to ranking these candidates. Are they likely to contain polymorphisms? We can assess the likelihood that they contain polymorphisms by mapping each transcript to see if any have strong cis QTLs. The logic of this search is that a transcript that has a strong cis-QTL is likely to contain functional polymorphisms that effect its own expression. This make is more like that the transcript is a ÒcausativeÓ factor since it is likely to be polymorphic.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0021_image089.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0021_image089.gif new file mode 100755 index 00000000..c76d7e43 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0021_image089.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0021_image090.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0021_image090.gif new file mode 100755 index 00000000..76eb790d --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0021_image090.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0021_image091.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0021_image091.gif new file mode 100755 index 00000000..2c10afe7 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0021_image091.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0021_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0021_notes_pane.htm new file mode 100755 index 00000000..e25a8134 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0021_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4><b>Candidate Genes: </b><span style="mso-spacerun: yes"> </span>The best we can do at this point is to make an educated guess about the candidacy status of all genes in the QTL support interval. For sake of argument, lets say that we are confident that the polymorphism is located between 130 and 150 Mb (20 Mb, equivalent to roughly 10 cM). There will typically be 12 to 15 genes per Mb, so we now would like to evaluate 240 to 300 positional candidates. We would like to highlight the biologically relevant subset of candidates. We could look through gene ontologies and expression levels to help us winnow the list. An alternate way avaiable using WebQTL is to generate a list of those genes in this 20 Mb interval that have transcripts that co-vary in expression with App expression.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>To do this, go back to the Trait Data and Editing window. Sort the correlations by position. Select Return = 500. Then scroll down the list to see positional candidates that share expression with App.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>There are several candidates that have high correlation with App even in this short 20 Mb interval. We can rank them by correlation, but they are all close.<span style="mso-spacerun: yes"> </span>There is one other imporant approach to ranking these candidates. Are they likely to contain polymorphisms? We can assess the likelihood that they contain polymorphisms by mapping each transcript to see if any have strong cis QTLs. The logic of this search is that a transcript that has a strong cis-QTL is likely to contain functional polymorphisms that effect its own expression. This make is more like that the transcript is a ÒcausativeÓ factor since it is likely to be polymorphic.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0022.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0022.htm new file mode 100755 index 00000000..014925b5 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0022.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0022.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:1.59%;left:3.97%;width:104.1%;height:13.78%; filter:DropShadow(Color=#000000, OffX=4, OffY=4)'> <div class=O style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:1.28%;left:1.27%;width:98.72%;height:88.46%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size: 233%;color:#E9EB5D'><i>Only one of these candidates is a functional </i></span></span><span style='position:absolute;top:46.37%;left:0%;width:85.69%'><span style='font-size:233%;color:#E9EB5D'><i>polymorphism</i></span></span></div> </div> <img border=0 src="slide0022_image092.gif" style='position:absolute;top:15.54%; left:2.64%;width:41.98%;height:84.45%'><img border=0 src="slide0022_image093.gif" style='position:absolute;top:31.44%;left:26.09%; width:27.15%;height:5.83%'> <div class=O style='position:absolute;top:28.09%;left:54.3%;width:50.06%; height:21.73%'> <div style='position:absolute;top:0%;left:0%;width:100.0%;height:25.2%'><span style='font-size:200%;color:#E9EB5D'><i>Hars2 = 0610006H08Rik<br> </i></span></div> <span style='position:absolute;top:24.39%;left:0%;width:94.7%'><span style='font-size:200%;color:#E9EB5D'><i>is a cis-QTL with a very </i></span></span><span style='position:absolute;top:49.59%;left:0%;width:84.39%'><span style='font-size:200%;color:#E9EB5D'><i>high likelihood ratio </i></span></span><span style='position:absolute;top:73.98%;left:0%;width:84.39%'><span style='font-size:200%;color:#E9EB5D'><i>statistic (LRS) score</i></span><span style='font-size:267%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>When you do this you will find that only the transcript 0610006H08Rik has a strong cis QTL. See the slide above. The LRS peaks above 35<span style="mso-spacerun: yes"> </span>(LOD of greater than 7.5). It turns out that this transcript is really Hars2, also known as histydl tRNA synthase 2.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0022_image092.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0022_image092.gif new file mode 100755 index 00000000..ce345af6 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0022_image092.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0022_image093.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0022_image093.gif new file mode 100755 index 00000000..fcb4d455 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0022_image093.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0022_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0022_notes_pane.htm new file mode 100755 index 00000000..5ab1a7fe --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0022_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>When you do this you will find that only the transcript 0610006H08Rik has a strong cis QTL. See the slide above. The LRS peaks above 35<span style="mso-spacerun: yes"> </span>(LOD of greater than 7.5). It turns out that this transcript is really Hars2, also known as histydl tRNA synthase 2.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0023.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0023.htm new file mode 100755 index 00000000..dac0fddc --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0023.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0023.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:1.59%;left:3.97%;width:104.1%;height:8.12%; filter:DropShadow(Color=#000000, OffX=4, OffY=4)'> <div class=O style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:2.17%;left:1.27%;width:98.85%;height:80.43%'><span style='font-size:233%;color:#E9EB5D'><i>Hars2 probe level analysis: 16 PMs mapped</i></span></div> </div> <img border=0 src="slide0023_image094.gif" style='position:absolute;top:10.77%; left:13.64%;width:72.58%;height:84.8%'><img border=0 src="slide0023_image095.gif" style='position:absolute;top:59.18%;left:2.38%; width:41.05%;height:36.74%'><img border=0 src="slide0023_image096.gif" style='position:absolute;top:60.07%;left:36.82%;width:26.75%;height:19.08%'><img border=0 src="slide0023_image097.gif" style='position:absolute;top:33.39%; left:21.19%;width:64.37%;height:2.65%'><img border=0 src="slide0023_image098.gif" style='position:absolute;top:35.68%;left:21.19%; width:64.37%;height:2.65%'><img border=0 src="slide0023_image099.gif" style='position:absolute;top:38.33%;left:21.19%;width:64.37%;height:2.65%'><img border=0 src="slide0023_image100.gif" style='position:absolute;top:19.78%; left:20.79%;width:28.74%;height:21.73%'> <div class=O style='position:absolute;top:28.09%;left:30.06%;width:4.9%; height:3.35%'><span style='font-size:117%;color:#FF0F0F'><i>SNP</i></span></div> <div class=O style='mso-line-spacing:"100 50 0";position:absolute;top:29.15%; left:40.13%;width:18.67%;height:3.35%'><span style='font-size:117%;color:#FF0F0F'>C in B6, T in D2 </span><span style='font-size:150%;color:black;mso-special-format: lastCR;display:none'><b><br> </b></span></div> <div class=O style='position:absolute;top:36.39%;left:50.99%;width:9.8%; height:3.35%'><span style='font-size:117%;color:#003399;mso-color-index:4'><i>no SNPs</i></span></div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>LetÕs look at Hars2 in more detail by mapping all of the perfect match probes (16 of them) that target this transcript.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Go back to the Trait Data and Editing window and select Chr 2 (rather than ALL as shown above) and also select PM Probes. Then click on Interval Mapping button.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>You will get the illustration above, but without the sequence data that we have added.<span style="mso-spacerun: yes"> </span>The 16 perfect match probes are arranged in sequence (red is 5 prime, blue is the 3 prime end). For example, the 5 prime-most primer 307387 has the sequence CACTG..... It also has a polymorphism at the 17 nucleotide of this 25 nt probe sequence.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>How do we know that the 5 prime probe is polymorphic? By looking up the sequence in the Celera Genomics databases which often contqains sequence data for C57BL/6J (B6 above) and for DBA/2J.<span style="mso-spacerun: yes"> </span>But two blue probes (14 and 15) do NOT contain SNPs but still have very large LRS scores. The other probes do not perform so wel. Highly variable probe performance is probably a result of the very different stacking energies of DNA-RNA duplexes.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0023_image094.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0023_image094.gif new file mode 100755 index 00000000..00e1c02c --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0023_image094.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0023_image095.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0023_image095.gif new file mode 100755 index 00000000..cd8bd524 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0023_image095.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0023_image096.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0023_image096.gif new file mode 100755 index 00000000..1191b566 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0023_image096.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0023_image097.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0023_image097.gif new file mode 100755 index 00000000..de56d1e8 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0023_image097.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0023_image098.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0023_image098.gif new file mode 100755 index 00000000..f84992a8 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0023_image098.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0023_image099.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0023_image099.gif new file mode 100755 index 00000000..719eb8e2 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0023_image099.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0023_image100.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0023_image100.gif new file mode 100755 index 00000000..2b932b21 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0023_image100.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0023_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0023_notes_pane.htm new file mode 100755 index 00000000..418d3b45 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0023_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>LetÕs look at Hars2 in more detail by mapping all of the perfect match probes (16 of them) that target this transcript.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Go back to the Trait Data and Editing window and select Chr 2 (rather than ALL as shown above) and also select PM Probes. Then click on Interval Mapping button.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>You will get the illustration above, but without the sequence data that we have added.<span style="mso-spacerun: yes"> </span>The 16 perfect match probes are arranged in sequence (red is 5 prime, blue is the 3 prime end). For example, the 5 prime-most primer 307387 has the sequence CACTG..... It also has a polymorphism at the 17 nucleotide of this 25 nt probe sequence.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>How do we know that the 5 prime probe is polymorphic? By looking up the sequence in the Celera Genomics databases which often contqains sequence data for C57BL/6J (B6 above) and for DBA/2J.<span style="mso-spacerun: yes"> </span>But two blue probes (14 and 15) do NOT contain SNPs but still have very large LRS scores. The other probes do not perform so wel. Highly variable probe performance is probably a result of the very different stacking energies of DNA-RNA duplexes.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0024.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0024.htm new file mode 100755 index 00000000..4c701e50 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0024.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Tissue differences in probe performance"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0024.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img border=0 src="slide0024_image101.gif" alt="Text Box: Tissue differences in probe performance" style='position:absolute; top:0%;left:-.79%;width:8.21%;height:89.92%'><img border=0 src="slide0024_image102.gif" style='position:absolute;top:58.48%;left:6.88%; width:62.78%;height:39.22%'> <div class=O style='position:absolute;top:17.66%;left:74.3%;width:21.32%; height:7.77%'><span style='font-family:"Gill Sans";font-size:300%;color:#E9EB5D'><i>Forebrain</i></span></div> <div class=O style='position:absolute;top:79.5%;left:74.3%;width:22.64%; height:7.77%'><span style='font-family:"Gill Sans";font-size:300%;color:#E9EB5D'><i>Stem cells</i></span></div> <img border=0 src="slide0024_image103.gif" style='position:absolute;top:28.97%; left:6.75%;width:62.78%;height:36.21%'><img border=0 src="slide0024_image104.gif" style='position:absolute;top:0%;left:6.62%; width:63.04%;height:36.39%'> <div class=O style='position:absolute;top:51.06%;left:73.5%;width:25.56%; height:7.77%'><span style='font-family:"Gill Sans";font-size:300%;color:#E9EB5D'><i>Cerebellum</i></span></div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The vertical text says it all: Even when using identical probes, mapping performance (and signal) depends on tissue type and mRNA complexity. This is another gene in the Hars2 interval. Forebrain and tem cell mRNAs were run on the same U74Av2 array, whereas the cerebellum mRNA was run on the 430A and 430B array set.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0024_image101.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0024_image101.gif new file mode 100755 index 00000000..0827d03e --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0024_image101.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0024_image102.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0024_image102.gif new file mode 100755 index 00000000..4da47c13 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0024_image102.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0024_image103.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0024_image103.gif new file mode 100755 index 00000000..05ef6183 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0024_image103.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0024_image104.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0024_image104.gif new file mode 100755 index 00000000..36c6885a --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0024_image104.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0024_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0024_notes_pane.htm new file mode 100755 index 00000000..3a7bdfa1 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0024_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The vertical text says it all: Even when using identical probes, mapping performance (and signal) depends on tissue type and mRNA complexity. This is another gene in the Hars2 interval. Forebrain and tem cell mRNAs were run on the same U74Av2 array, whereas the cerebellum mRNA was run on the 430A and 430B array set.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0025.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0025.htm new file mode 100755 index 00000000..238b554b --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0025.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Is there known biology to link Hars2 with App? "> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0025.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:-3.53%;left:2.11%;width:96.42%;height:18.55%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";mso-margin-left-alt:232; mso-text-indent-alt:0;position:absolute;top:30.47%;left:.96%;width:97.39%; height:35.23%'><span style='font-size:68%'><i>Is there known biology to link Hars2 with App? </i></span></div> </div> <div style='position:absolute;top:82.15%;left:4.1%;width:96.42%;height:18.55%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'></div> <div class=O style='position:absolute;top:62.54%;left:5.16%;width:29.13%; height:12.36%'> <div style='position:absolute;top:0%;left:0%;width:100.0%;height:34.28%'><span style='font-size:150%;color:#E9EB5D;mso-color-index:3'><b>69 SNPs, 1 cSNP: <br> </b></span></div> <div style='position:absolute;top:32.85%;left:0%;width:96.81%;height:34.28%'><span style='font-size:150%;color:#E9EB5D;mso-color-index:3'><b>6 exons in NCBI, <br> </b></span></div> <div style='position:absolute;top:65.71%;left:0%;width:100.0%;height:34.28%'><span style='font-size:150%;color:#E9EB5D;mso-color-index:3'><b>2 exons in Celera</b></span></div> </div> <img border=0 src="slide0025_image105.gif" style='position:absolute;top:9.54%; left:3.31%;width:60.79%;height:42.57%'><img border=0 src="slide0025_image106.gif" style='position:absolute;top:28.62%;left:40.0%; width:55.76%;height:69.78%'> <div class=O style='position:absolute;top:14.13%;left:69.4%;width:23.84%; height:6.53%'><span style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D'><i><span style="mso-spacerun: yes"> </span>Not obvious</i></span></div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Hars2 is not a well characterized gene and their is no biology yet to support the hypothesis that Hars2 modulates gene expression, let alone App expression in specific. There are also serious database/assembly discrepancies between Celera and MGSCv3 regarding the genomic organization of this gene. But there appear to be approximately 69 SNPs in Hars2, one of which results in a substitution.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0025_image105.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0025_image105.gif new file mode 100755 index 00000000..242e4087 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0025_image105.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0025_image106.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0025_image106.gif new file mode 100755 index 00000000..c1453aee --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0025_image106.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0025_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0025_notes_pane.htm new file mode 100755 index 00000000..ef04157c --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0025_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Hars2 is not a well characterized gene and their is no biology yet to support the hypothesis that Hars2 modulates gene expression, let alone App expression in specific. There are also serious database/assembly discrepancies between Celera and MGSCv3 regarding the genomic organization of this gene. But there appear to be approximately 69 SNPs in Hars2, one of which results in a substitution.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0026.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0026.htm new file mode 100755 index 00000000..4225db8a --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0026.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: WebQTL link to www.webqtl.org/search.html"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0026.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:3.0%;left:2.11%;width:96.42%;height:19.61%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";mso-margin-left-alt:232; mso-text-indent-alt:0;position:absolute;top:0%;left:.96%;width:97.39%; height:100.0%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size:68%'><i>WebQTL<span style="mso-spacerun: yes"> </span><br> </i></span></span><span style='position: absolute;top:32.43%;left:4.37%;width:95.76%'><span style='font-size:68%'><i>link to <br> </i></span></span><span style='position:absolute;top:58.55%;left:4.37%; width:95.76%'><span style='font-size:86%'><i>www.webqtl.org/search.html</i></span><span style='font-size:68%;mso-special-format:lastCR;display:none'><i><br> </i></span></span></div> </div> <div style='position:absolute;top:36.57%;left:2.51%;width:73.24%;height:45.05%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='position:absolute;top:0%;left:2.71%;width:97.28%; height:81.96%'> <div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:0%;left:0%;width:94.6%;height:31.57%'><span style='position:absolute;top:0%;left:7.46%;width:92.53%'><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'><span style='mso-special-format: "numbullet3\,1";color:#FBFDB8;position:absolute;left:-8.06%;font-family:Times; font-size:99%'>1.</span></span><span style='font-size:94%;color:#E9EB5D; mso-color-index:3'>Discovering shared expression </span></span><span style='position:absolute;top:43.93%;left:7.46%;width:82.12%'><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>patterns<br> </span></span></div> <div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:41.14%;left:0%;width:84.94%;height:31.57%'><span style='position:absolute;top:0%;left:8.31%;width:91.46%'><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'><span style='mso-special-format: "numbullet3\,2";color:#FBFDB8;position:absolute;left:-9.09%;font-family:Times; font-size:99%'>2.</span></span><span style='font-size:94%;color:#E9EB5D; mso-color-index:3'>Discovering upstream </span></span><span style='position: absolute;top:43.93%;left:8.31%;width:91.46%'><span style='font-size:94%; color:#E9EB5D;mso-color-index:3'>modulators (QTLs)<br> </span></span></div> <div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:82.29%;left:0%;width:100.0%;height:17.7%'><span style='position:absolute;top:0%;left:7.06%;width:92.75%'><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'><span style='mso-special-format: "numbullet3\,3";color:#FBFDB8;position:absolute;left:-7.61%;font-family:Times; font-size:99%'>3.</span></span><span style='font-size:94%;color:#E9EB5D; mso-color-index:3'>Discovering downstream targets</span></span></div> </div> </div> <div style='position:absolute;top:82.15%;left:4.1%;width:96.42%;height:18.55%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'></div> <img border=0 src="slide0026_image107.gif" style='position:absolute;top:65.9%; left:65.29%;width:26.35%;height:10.77%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Part 3.<span style="mso-spacerun: yes"> </span>Many investigators would like to discover the set of downstream targets of a gene of interest.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>In a genetic and functional sense, that question can only be addressed effectively if there is genetic variation in the particular gene.<span style="mso-spacerun: yes"> </span>We know that Fos is an important transcription factor, but unless it is polymorphic between C57BL/6J and DBA/2J, then it cannot generate a genetic variance signal with which we can work. We can still study covariance of Fos and hundreds of other transcripts (an interesting exercise), but there are no genetic causes-and-effects.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0026_image107.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0026_image107.gif new file mode 100755 index 00000000..e26b7a56 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0026_image107.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0026_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0026_notes_pane.htm new file mode 100755 index 00000000..138a5dca --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0026_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Part 3.<span style="mso-spacerun: yes"> </span>Many investigators would like to discover the set of downstream targets of a gene of interest.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>In a genetic and functional sense, that question can only be addressed effectively if there is genetic variation in the particular gene.<span style="mso-spacerun: yes"> </span>We know that Fos is an important transcription factor, but unless it is polymorphic between C57BL/6J and DBA/2J, then it cannot generate a genetic variance signal with which we can work. We can still study covariance of Fos and hundreds of other transcripts (an interesting exercise), but there are no genetic causes-and-effects.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0027.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0027.htm new file mode 100755 index 00000000..7701ce1a --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0027.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Requirement: The gene must be polymorphic to be genetically ÒupstreamÓ"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0027.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:2.29%;left:2.51%;width:108.47%;height:18.9%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";position:absolute;top:7.47%; left:1.22%;width:98.77%;height:85.04%'><span style='position:absolute; top:0%;left:0%;width:100.0%'><span style='font-size:82%'><i>Requirement: The gene must be polymorphic to </i></span></span><span style='position:absolute; top:51.64%;left:3.7%;width:79.72%'><span style='font-size:82%'><i>be genetically ÒupstreamÓ</i></span><span style='font-size:82%;mso-special-format: lastCR;display:none'><br> </span></span></div> </div> <div style='position:absolute;top:21.37%;left:2.51%;width:84.5%;height:15.01%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";position:absolute;top:32.94%; left:1.56%;width:98.43%;height:40.0%'><span style='font-size:64%'><i>What are targets of the Hars2 polymorphisms?</i></span><span style='font-size:82%; mso-special-format:lastCR;display:none'><br> </span></div> </div> <img border=0 src="slide0027_image108.gif" style='position:absolute;top:33.92%; left:1.72%;width:49.66%;height:32.15%'><img border=0 src="slide0027_image109.gif" style='position:absolute;top:33.39%;left:53.37%; width:44.23%;height:58.65%'> <div class=O style='position:absolute;top:69.96%;left:7.54%;width:51.39%; height:21.2%'> <div style='position:absolute;top:0%;left:0%;width:84.02%;height:32.5%'><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>App and many other<br> </i></span></div> <span style='position:absolute;top:33.33%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>correlated transcripts and </i></span></span><span style='position:absolute;top:67.5%; left:0%;width:84.02%'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>other traits.</i></span></span></div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Genes must be polymorphic to generate downstream genetic effects (as opposed to downstream molecular effects). Hars2 meets this condition because we have already mapped a functional polymorphism in the gene. We can therefore posit that Hars2 is a QT gene. What transcripts are downstream? <i>App</i> is one obvious candidate, but there are many more.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The are several ways to look for downstream targets. The best and most obvious is to look up all transcripts that have high correlations with Hars2 itself. You should know how to do this. An alternative method is shown here for teaching purpose and to show you what to do if your gene of interest is not in our database. You need to know:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Times size=3>1.</font><font face=Verdana size=3> Where your gene is located. You need this information to find a surrogate marker; a marker that is located very close to your gene of interest.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. That your gene is polymorphic between C57BL/6J and DBA/2J.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>LetÕs look at the correlation of Hars2 with BXD genotypes as shown in the slide above to illustrate how to use markers as surrogate traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Go to the Trait Date and Editing window one more time. We want the data for Hars2 this time, not App. You should be able to show that Hars2 has a high<span style="mso-spacerun: yes"> </span>correlation with D2Mit423 as shown in the slide above.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>By clicking on the symbol D2Mit423 in the Correlation window, you will generate a new Trait Data window shown on the next slide.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0027_image108.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0027_image108.gif new file mode 100755 index 00000000..c4a27e18 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0027_image108.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0027_image109.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0027_image109.gif new file mode 100755 index 00000000..c03ea994 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0027_image109.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0027_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0027_notes_pane.htm new file mode 100755 index 00000000..9614c538 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0027_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Genes must be polymorphic to generate downstream genetic effects (as opposed to downstream molecular effects). Hars2 meets this condition because we have already mapped a functional polymorphism in the gene. We can therefore posit that Hars2 is a QT gene. What transcripts are downstream? <i>App</i> is one obvious candidate, but there are many more.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The are several ways to look for downstream targets. The best and most obvious is to look up all transcripts that have high correlations with Hars2 itself. You should know how to do this. An alternative method is shown here for teaching purpose and to show you what to do if your gene of interest is not in our database. You need to know:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Times size=2>1.</font><font face=Verdana size=2> Where your gene is located. You need this information to find a surrogate marker; a marker that is located very close to your gene of interest.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2. That your gene is polymorphic between C57BL/6J and DBA/2J.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>LetÕs look at the correlation of Hars2 with BXD genotypes as shown in the slide above to illustrate how to use markers as surrogate traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Go to the Trait Date and Editing window one more time. We want the data for Hars2 this time, not App. You should be able to show that Hars2 has a high<span style="mso-spacerun: yes"> </span>correlation with D2Mit423 as shown in the slide above.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>By clicking on the symbol D2Mit423 in the Correlation window, you will generate a new Trait Data window shown on the next slide.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0028.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0028.htm new file mode 100755 index 00000000..28930694 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0028.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Direct correlations between genotypes and traits"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0028.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:-1.23%;left:2.51%;width:110.06%;height:11.66%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";position:absolute;top:16.66%; left:1.2%;width:98.79%;height:66.66%'><span style='font-size:82%'><i>Direct correlations between genotypes and traits</i></span><span style='font-size: 82%;mso-special-format:lastCR;display:none'><br> </span></div> </div> <div class=O style='position:absolute;top:22.43%;left:3.44%;width:34.83%; height:42.4%'> <div style='position:absolute;top:0%;left:0%;width:100.0%;height:16.25%'><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>App and<br> </i></span></div> <span style='position:absolute;top:16.66%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>correlated traits </i></span></span><span style='position:absolute;top:33.33%;left:0%; width:100.0%'><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>would be obvious </i></span></span><span style='position:absolute;top:50.0%; left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>candidates to </i></span></span><span style='position:absolute; top:67.08%;left:0%;width:100.0%'><span style='font-family:"Gill Sans"; font-size:267%;color:#E9EB5D'><i>correlate with </i></span></span><span style='position:absolute;top:83.75%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>D2Mit423</i></span></span></div> <img border=0 src="slide0028_image110.gif" style='position:absolute;top:10.07%; left:33.37%;width:40.0%;height:87.63%'><img border=0 src="slide0028_image111.gif" style='position:absolute;top:82.68%;left:65.29%; width:14.7%;height:7.24%'> <div class=O style='position:absolute;top:79.68%;left:82.11%;width:13.11%; height:13.95%'> <div style='position:absolute;top:0%;left:0%;width:100.0%;height:49.36%'><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>B = -1<br> </i></span></div> <div style='position:absolute;top:50.63%;left:0%;width:94.94%;height:49.36%'><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>D = 1</i></span></div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>We can review the set of correlations between the marker D2Mit423 and all transcripts in forebrain.<span style="mso-spacerun: yes"> </span>This is in essence a backwards way of mapping QTLs. We are considering one marker and asking what traits correlate to the marker and how well.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0028_image110.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0028_image110.gif new file mode 100755 index 00000000..f70a8f8b --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0028_image110.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0028_image111.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0028_image111.gif new file mode 100755 index 00000000..426065e3 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0028_image111.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0028_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0028_notes_pane.htm new file mode 100755 index 00000000..89b67431 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0028_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>We can review the set of correlations between the marker D2Mit423 and all transcripts in forebrain.<span style="mso-spacerun: yes"> </span>This is in essence a backwards way of mapping QTLs. We are considering one marker and asking what traits correlate to the marker and how well.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0029.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0029.htm new file mode 100755 index 00000000..0bb9da8b --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0029.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: WhatÕs downstream of Chr 2 near Hars2?"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0029.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:-.35%;left:2.51%;width:96.95%;height:11.66%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";position:absolute;top:16.66%; left:1.36%;width:98.77%;height:66.66%'><span style='font-size:82%'><i>WhatÕs downstream of Chr 2 near Hars2?</i></span><span style='font-size:82%; mso-special-format:lastCR;display:none'><br> </span></div> </div> <img border=0 src="slide0029_image112.gif" style='position:absolute;top:9.54%; left:1.98%;width:83.04%;height:79.5%'> <div style='position:absolute;top:86.92%;left:2.51%;width:111.12%;height:11.66%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";position:absolute;top:27.27%; left:1.19%;width:98.8%;height:51.51%'><span style='font-size:64%'><i>Notice many Chr 2 hits: Linkage disequilibrium limits specificity</i></span><span style='font-size:64%;mso-special-format:lastCR;display:none'><br> </span></div> </div> <img border=0 src="slide0029_image113.gif" style='position:absolute;top:27.03%; left:7.01%;width:22.38%;height:17.49%'> <div class=O style='position:absolute;top:24.73%;left:27.68%;width:16.82%; height:4.24%'><span style='font-size:150%;color:#FF0F0F'><b>Click here</b></span></div> <img border=0 src="slide0029_image114.gif" style='position:absolute;top:39.22%; left:48.21%;width:12.18%;height:5.47%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The marker D2Mit423 correlates moderately well with a number of Chr 2 transcripts. This is due to linkage disequilibrium. These correlations are not due to a molecular interactions other than being close together on a chromosome.<span style="mso-spacerun: yes"> </span>But we have circled one transcript, actinin alpha 2, that has a moderately good correlation (0.59) with D2Mit423. If we map this gene we expect to find a suggestive QTL that peaks near D2Mit423</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0029_image112.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0029_image112.gif new file mode 100755 index 00000000..c1fcf2db --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0029_image112.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0029_image113.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0029_image113.gif new file mode 100755 index 00000000..a5bebbe9 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0029_image113.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0029_image114.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0029_image114.gif new file mode 100755 index 00000000..9a070a5b --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0029_image114.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0029_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0029_notes_pane.htm new file mode 100755 index 00000000..62c56ca6 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0029_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The marker D2Mit423 correlates moderately well with a number of Chr 2 transcripts. This is due to linkage disequilibrium. These correlations are not due to a molecular interactions other than being close together on a chromosome.<span style="mso-spacerun: yes"> </span>But we have circled one transcript, actinin alpha 2, that has a moderately good correlation (0.59) with D2Mit423. If we map this gene we expect to find a suggestive QTL that peaks near D2Mit423</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0030.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0030.htm new file mode 100755 index 00000000..e3dec4be --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0030.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: WhatÕs downstream of Chr 2 near Hars2?"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0030.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:-.35%;left:2.51%;width:96.95%;height:11.66%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";position:absolute;top:16.66%; left:1.36%;width:98.77%;height:66.66%'><span style='font-size:82%'><i>WhatÕs downstream of Chr 2 near Hars2?</i></span><span style='font-size:82%; mso-special-format:lastCR;display:none'><br> </span></div> </div> <img border=0 src="slide0030_image115.gif" style='position:absolute;top:12.19%; left:7.54%;width:61.58%;height:75.61%'> <div class=O style='position:absolute;top:90.1%;left:5.16%;width:107.01%; height:6.0%'><span style='font-family:"Gill Sans";font-size:233%;color:#E9EB5D'><i>modest support that Actn2 is modulated by the Hars2 region</i></span></div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>There is some support for the hypothesis that Actn2 is downstream of a polymorphism in the Hars2 region. But again, due to the 10 to 20 Mb precision of the mapping data, this relation could be generated by a large number of other polymorphisms close to Hars2. In the absence of a biological connection between Actn2 and Hars2 we have a weak hypothesis. If there were a plausible functional connection between the two genes, then this hypothesis could be quickly upgraded.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0030_image115.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0030_image115.gif new file mode 100755 index 00000000..48462fa6 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0030_image115.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0030_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0030_notes_pane.htm new file mode 100755 index 00000000..88bd6165 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0030_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>There is some support for the hypothesis that Actn2 is downstream of a polymorphism in the Hars2 region. But again, due to the 10 to 20 Mb precision of the mapping data, this relation could be generated by a large number of other polymorphisms close to Hars2. In the absence of a biological connection between Actn2 and Hars2 we have a weak hypothesis. If there were a plausible functional connection between the two genes, then this hypothesis could be quickly upgraded.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0031.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0031.htm new file mode 100755 index 00000000..b07ce4c2 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0031.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Does Hars2 correlate with Actn2 strongly?"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0031.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:-1.23%;left:2.51%;width:95.49%;height:9.01%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";position:absolute;top:13.72%; left:1.38%;width:97.22%;height:76.47%'><span style='font-size:73%'><i>Does Hars2 correlate with Actn2 strongly?</i></span><span style='font-size:82%; mso-special-format:lastCR;display:none'><br> </span></div> </div> <img border=0 src="slide0031_image116.gif" style='position:absolute;top:7.06%; left:2.78%;width:47.15%;height:28.97%'><img border=0 src="slide0031_image117.gif" style='position:absolute;top:33.21%;left:30.06%; width:67.41%;height:66.78%'><img border=0 src="slide0031_image118.gif" style='position:absolute;top:17.49%;left:33.24%;width:15.36%;height:15.9%'> <div class=O style='position:absolute;top:41.87%;left:2.64%;width:28.47%; height:42.4%'><span style='position:absolute;top:0%;left:0%;width:94.41%'><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>Plenty of high </i></span></span><span style='position:absolute;top:16.66%;left:0%;width:89.76%'><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>correlations, </i></span></span><span style='position:absolute;top:33.75%;left:0%;width:89.76%'><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>including 2 </i></span></span><span style='position:absolute;top:50.41%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>actins, but not </i></span></span><span style='position:absolute;top:67.08%;left:0%;width:89.76%'><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>to Actn2 </i></span></span><span style='position:absolute;top:83.75%;left:0%;width:89.76%'><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>specifically.</i></span></span></div> <div class=O style='position:absolute;top:16.43%;left:52.84%;width:25.03%; height:6.89%'><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>Sort by gene</i></span></div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>We can test the Hars2 to Actn2 connection directly. This process weakens the putative association. We are ready to move on and examine other candidates in the Hars2 region near D2Mit423.<span style="mso-spacerun: yes"> </span>Or in your case, please start from the beginning using other genes and transcripts and tissues that interest you more than this App-Hsp84-Hars2 example.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>This concludes the first demonstation of how to use some of the WebQTL features. Please explore. Please also send feedback for improvements or additions to rwilliam@nb.utmem.edu</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0031_image116.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0031_image116.gif new file mode 100755 index 00000000..7e1dd508 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0031_image116.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0031_image117.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0031_image117.gif new file mode 100755 index 00000000..bbc776f5 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0031_image117.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0031_image118.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0031_image118.gif new file mode 100755 index 00000000..31efe2e2 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0031_image118.gif Binary files differdiff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0031_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0031_notes_pane.htm new file mode 100755 index 00000000..435ca8e2 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0031_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>We can test the Hars2 to Actn2 connection directly. This process weakens the putative association. We are ready to move on and examine other candidates in the Hars2 region near D2Mit423.<span style="mso-spacerun: yes"> </span>Or in your case, please start from the beginning using other genes and transcripts and tissues that interest you more than this App-Hsp84-Hars2 example.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>This concludes the first demonstation of how to use some of the WebQTL features. Please explore. Please also send feedback for improvements or additions to rwilliam@nb.utmem.edu</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0032.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0032.htm new file mode 100755 index 00000000..60a1bee2 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0032.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Contact for comments and improvements:"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0032.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:2.29%;left:2.51%;width:94.7%;height:10.24%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";position:absolute;top:18.96%; left:1.39%;width:97.2%;height:67.24%'><span style='font-size:73%'><i>Contact for comments and improvements:</i></span><span style='font-size:82%;mso-special-format: lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:12.54%;left:6.62%;width:90.59%;height:32.68%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 ";position:absolute;top:0%; left:1.46%;width:96.92%;height:100.0%'><span style='position:absolute; top:0%;left:0%;width:100.0%'><span style='font-size:82%'>rwilliam@ nb.utmem.edu<br> </span></span><span style='position:absolute;top:25.4%; left:4.67%;width:95.47%'><span style='font-size:82%'>kenneth.manly@roswellpark.org<br> </span></span><span style='position:absolute;top:50.81%;left:4.67%;width:95.47%'><span style='font-size:82%'>lulu@ nb.utmem.edu<br> </span></span><span style='position:absolute;top:75.67%;left:4.67%;width:95.47%'><span style='font-size:82%'>echesler@ nb.utmem.edu</span></span></div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>END</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0032_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0032_notes_pane.htm new file mode 100755 index 00000000..2af93a35 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0032_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <link id=Main-File rel=Main-File href="WebQTLDemo.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>END</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0033.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0033.htm new file mode 100755 index 00000000..62f15daa --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0033.htm @@ -0,0 +1,153 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: WebQTL Demonstration One please link to www.webqtl.org/search.html"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0033.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; 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+</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0.03 * g_width; myheight = 0.19 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.19 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt:232; mso-text-indent-alt:0;mso-line-spacing:" 0 ";mso-margin-left-alt:232; mso-text-indent-alt:0'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:68%'><i>WebQTL Demonstration One<br> </i></span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0.03 * g_width; myheight = 0.06 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:68%'><i>please link to <br> </i></span></span></layer><script> + mytop = 0.11 * g_height; myleft = 0.03 * g_width; myheight = 0.08 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:86%'><i>www.webqtl.org/search.html</i></span><span style='font-size:68%;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </layer><script> + mytop = 0.31 * g_height; myleft = 0.05 * g_width; myheight = 0.45 * g_height; mywidth = 0.73 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.42 * g_height; mywidth = 0.71 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.16 * g_height; mywidth = 0.63 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.63 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part 1: How to discover shared </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.55 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>expression patterns (slides </span></span></layer><script> + mytop = 0.1 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.55 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>2Ð14)<br> </span></span></layer></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.6 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.6 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part 2. 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mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:"Arial Rounded MT Bold";font-size:233%;color:#6E6E6E'>RNA</span><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; display:none'><br> </span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.76 * g_height; myleft = 0.04 * g_width; myheight = 0.13 * g_height; mywidth = 0.78 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.77 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:250%; color:#E9EB5D;mso-color-index:3'><i>PowerPoint ÒNormal viewÓ has notes that </i></span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.78 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:250%; color:#E9EB5D;mso-color-index:3'><i>may be useful companions to these slides.</i></span><span style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D;mso-color-index: 3;mso-special-format:lastCR;display:none'><br> </span></span></layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Welcome to a short demonstation of WebQTL. Please adjust the wize of windows on your monitor so that you can see part of this page as well as WebQTL windows. WebQTL will produce a potentially large number of new windows (pop-ups), so you may need to modify your browser preferences to permit pop-ups.<span style="mso-spacerun: yes"> </span>In this demonstration, we explore one important transcript expressed in the brain: the amyloid beta precursor protein messenger RNA. The product of this mRNA, the APP protein, is associated with Alzheimer disease.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>(Initial version of June 2003 by Rob Williams, Last edits June 16, 2003 by RW.)</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0034.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0034.htm new file mode 100755 index 00000000..343c0d37 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0034.htm @@ -0,0 +1,151 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); 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myheight = 0.07 * g_height; mywidth = 0.2 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.42 * g_width; +yy = 0.49 * g_height; +ht = 0.07 * g_height; +wd = 0.2 * g_width; +document.write( +'<img border=0 src="slide0002_image003.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.5 * g_height; myleft = 0.62 * g_width; myheight = 0.36 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.62 * g_width; +yy = 0.5 * g_height; +ht = 0.36 * g_height; +wd = 0.15 * g_width; +document.write( +'<img border=0 src="slide0002_image004.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.6 * g_height; myleft = 0.79 * g_width; myheight = 0.11 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'>choose a<br> </span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'>database</span></div> </layer></div> </layer><script> + mytop = 0.46 * g_height; myleft = 0.79 * g_width; myheight = 0.11 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'>enter<br> </span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'><i>amyloid beta</i></span><span style='font-family:"Gill Sans"; font-size:250%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.78 * g_height; myleft = 0.79 * g_width; myheight = 0.11 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'>select<br> </span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'>search</span></div> </layer></div> </layer><script> + mytop = 0 * g_height; myleft = 0.03 * g_width; myheight = 0.09 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div> <layer> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'></div> </layer> <script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:0;mso-line-spacing:" 0 ";mso-margin-left-alt:348; mso-text-indent-alt:0'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>link to www.webqtl.org/search.html</span></div> </layer></div> </layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>WebQTL can be used to enter your own trait data or to work with data that we have entered for you.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Linking to http://www.webqtl.org/search.html will get you a version of the window above. It may not be identical in layout but it will have the key features. Please follow the intructions on the slide. Of course, we encourage you to enter your own terms of interest.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Two points: If you make a search term too complex you may get no hits. if you make it too simple (for example, APP) then you may get too much. Experiment.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>If you just link to</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>http://www.webqtl.org you will NOT see the window above but will see text that will help you to enter your own data.<span style="mso-spacerun: yes"> </span>To get to a version of the window shown above you will need to click on the phrase<span style="mso-spacerun: yes"> </span>RNA expression and Phenotype Databases in the upper banner.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>If you do not get a new page within 30 seconds then there is<span style="mso-spacerun: yes"> </span>a problem: try the mirror site http://webqtl.org/search.html.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0035.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0035.htm new file mode 100755 index 00000000..c53c9bbc --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0035.htm @@ -0,0 +1,116 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Search results"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0035.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.09 * g_height; myleft = 0.09 * g_width; myheight = 0.87 * g_height; mywidth = 0.59 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.09 * g_width; +yy = 0.09 * g_height; +ht = 0.87 * g_height; +wd = 0.59 * g_width; +document.write( +'<img border=0 src="slide0003_image005.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.72 * g_height; myleft = 0.14 * g_width; myheight = 0.06 * g_height; mywidth = 0.62 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.14 * g_width; +yy = 0.72 * g_height; +ht = 0.06 * g_height; +wd = 0.62 * g_width; +document.write( +'<img border=0 src="slide0003_image006.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.68 * g_height; myleft = 0.78 * g_width; myheight = 0.17 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'>highlight<br> </span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'><i>amyloid beta<br> </i></span></div> </layer><script> + mytop = 0.11 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'>then click</span><span style='font-family:"Gill Sans"; font-size:250%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = -0.04 * g_height; myleft = 0.07 * g_width; myheight = 0.18 * g_height; mywidth = 0.84 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.04 * g_height; myleft = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 0.82 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%'><span style='font-size:91%'>Search results</span><span style='mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>If all goes well, you will see a version of this window. WebQTL will display up to about 100 hits. If a search generates larger numbers of hits then you will need to refine your search terms.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0036.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0036.htm new file mode 100755 index 00000000..ae7843aa --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0036.htm @@ -0,0 +1,122 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0036.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.14 * g_height; mywidth = 0.97 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.95 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";mso-margin-left-alt:348; mso-text-indent-alt:56'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>First page of data: The ÒTrait Data FormÓ</span></div> </layer></div> </layer><script> + mytop = 0.11 * g_height; myleft = 0.03 * g_width; myheight = 0.86 * g_height; mywidth = 0.77 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.03 * g_width; +yy = 0.11 * g_height; +ht = 0.86 * g_height; +wd = 0.77 * g_width; +document.write( +'<img border=0 src="slide0004_image007.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.56 * g_height; myleft = 0.66 * g_width; myheight = 0.07 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.66 * g_width; +yy = 0.56 * g_height; +ht = 0.07 * g_height; +wd = 0.14 * g_width; +document.write( +'<img border=0 src="slide0004_image008.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.5 * g_height; myleft = 0.81 * g_width; myheight = 0.27 * g_height; mywidth = 0.2 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.2 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-size:200%;color:#E9EB5D'><i>Click here<br> </i></span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-size:200%;color:#E9EB5D'><i>to learn<br> </i></span></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-size:200%;color:#E9EB5D'><i>about<br> </i></span></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-size:200%;color:#E9EB5D'><i>data<br> </i></span></div> </layer><script> + mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-size:200%;color:#E9EB5D'><i>source</i></span></div> </layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The Trait Data and Editing Form is the single more important page from the point of view of working with WebQTL data. Please read the text carefully. Explore the links, but do not close this page. We will need it many more times in this demonstration.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0037.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0037.htm new file mode 100755 index 00000000..bb776db5 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0037.htm @@ -0,0 +1,93 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0037.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.01 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";mso-margin-left-alt:348; mso-text-indent-alt:56'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Data sources: Phenotpyes and genotypes</span></div> </layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.07 * g_width; myheight = 0.88 * g_height; mywidth = 0.84 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.07 * g_width; +yy = 0.1 * g_height; +ht = 0.88 * g_height; +wd = 0.84 * g_width; +document.write( +'<img border=0 src="slide0005_image009.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>There are already five databases in WebQTL. Each will eventually have a page like this describing the data source and appropriate citations to these databases. The great majority of data in WebQTL were generated in our own labs and those of our collaborators.<span style="mso-spacerun: yes"> </span>We welcome you to use these data, but caution you that there are inevitably lots of little problems and issues that may compromise some results. Be cautious and skeptical. Ask us questions before you leap to publication. And please, if you find the data useful or can verify or refute data, LET US KNOW. We would like to add you to our reference section and add links to improvements.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0038.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0038.htm new file mode 100755 index 00000000..b3e613ca --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0038.htm @@ -0,0 +1,119 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0038.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.47 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.05 * g_height; mywidth = 0.45 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";mso-margin-left-alt:348; mso-text-indent-alt:56'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:81%;color:#E9EB5D;mso-color-index:3'>Return to Trait Data page </span></div> </layer></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.79 * g_height; mywidth = 0.48 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0 * g_width; +yy = 0.07 * g_height; +ht = 0.79 * g_height; +wd = 0.48 * g_width; +document.write( +'<img border=0 src="slide0006_image010.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.5 * g_width; myheight = 0.78 * g_height; mywidth = 0.48 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.5 * g_width; +yy = 0.07 * g_height; +ht = 0.78 * g_height; +wd = 0.48 * g_width; +document.write( +'<img border=0 src="slide0006_image011.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.01 * g_height; myleft = 0.52 * g_width; myheight = 0.13 * g_height; mywidth = 0.43 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.05 * g_height; mywidth = 0.4 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";mso-margin-left-alt:348; mso-text-indent-alt:56'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:81%;color:#E9EB5D;mso-color-index:3'>bottom of this page</span></div> </layer></div> </layer><script> + mytop = 0.86 * g_height; myleft = 0.03 * g_width; myheight = 0.11 * g_height; mywidth = 1.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>Trait data for each strain with SE when known. For array data </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>the scale is ~ log base 2.<span style="mso-spacerun: yes"> </span></span><span style='font-size: 183%;color:#E9EB5D;mso-color-index:3'>F1=13.752 = 2^13.752 = 13796 </span><span style='font-family:"Gill Sans";font-size:183%;color:#E9EB5D;mso-color-index: 3;mso-special-format:lastCR;display:none'><br> </span></span></layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>This<span style="mso-spacerun: yes"> </span>slide shows you the<span style="mso-spacerun: yes"> </span>lower parts of the Trait Data Page. We expect to make many small modification of this page, so do not be surprised if some elements have been moved around.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0039.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0039.htm new file mode 100755 index 00000000..0b96295c --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0039.htm @@ -0,0 +1,104 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0039.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.01 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";mso-margin-left-alt:348; mso-text-indent-alt:56'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Discovering shared expression patterns</span></div> </layer></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0.05 * g_width; myheight = 0.55 * g_height; mywidth = 0.86 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.05 * g_width; +yy = 0.16 * g_height; +ht = 0.55 * g_height; +wd = 0.86 * g_width; +document.write( +'<img border=0 src="slide0007_image012.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.6 * g_height; myleft = 0.45 * g_width; myheight = 0.14 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.45 * g_width; +yy = 0.6 * g_height; +ht = 0.14 * g_height; +wd = 0.13 * g_width; +document.write( +'<img border=0 src="slide0007_image013.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Finally, we can now start an analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>We ask a simple question:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Do differences in App transcript expression correlate with those of any other transcripts in the forebrain?</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0040.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0040.htm new file mode 100755 index 00000000..a71d67b3 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0040.htm @@ -0,0 +1,111 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0040.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.01 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.9 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";mso-margin-left-alt:348; mso-text-indent-alt:56'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>The </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> transcript neighborhood</span></div> </layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.05 * g_width; myheight = 0.88 * g_height; mywidth = 0.66 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.05 * g_width; +yy = 0.1 * g_height; +ht = 0.88 * g_height; +wd = 0.66 * g_width; +document.write( +'<img border=0 src="slide0008_image014.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.3 * g_height; myleft = 0.75 * g_width; myheight = 0.18 * g_height; mywidth = 0.26 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.24 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:150%;color:#E9EB5D;mso-color-index: 3'><b>Question: </b></span><span style='font-size:133%;color:#E9EB5D; mso-color-index:3'><b>How </b></span></span></layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.25 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:133%;color:#E9EB5D;mso-color-index: 3'><b>many transcripts </b></span></span></layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.26 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:133%;color:#E9EB5D;mso-color-index: 3'><b>have correlations </b></span></span></layer><script> + mytop = 0.11 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.25 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:133%;color:#E9EB5D;mso-color-index: 3'><b>>0.7? What does </b></span></span></layer><script> + mytop = 0.14 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.22 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:133%;color:#E9EB5D;mso-color-index: 3'><b>this imply.</b></span></span></layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The answer is a strong Yes. A very large number of transcripts have correlations above 0.7 (absolute value) with App mRNA. The precise number today is 208. But this will change as we add more strains and arrays. In any case, this is a fairly large number and all of these correlations are significant at alpha .05 even when correcting for the enormous numbers<span style="mso-spacerun: yes"> </span>of tests (12422 tests).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>What does this imply?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>That there can be massive codependence of expression variance among transcripts. App is NOT an isolated instance. This is improtant biologically and statistically. From a statistical perspective, we would like to know how many ÒindependentÓ test we effectively are performing when we use array data in this way. Are we testing 12000 independent transcripts or just 1200 transcriptional ÒmodulesÓ each with blurred boarders but each with about 10 effective members. There is no answer yet, but we probaby have a large enough data set to begin to answer this question.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0041.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0041.htm new file mode 100755 index 00000000..df4bc799 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0041.htm @@ -0,0 +1,93 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0041.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.02 * g_height; myleft = 0.06 * g_width; myheight = 0.14 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.92 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";mso-margin-left-alt:348; mso-text-indent-alt:56'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Handdrawn sketch of the neighborhood</span></div> </layer></div> </layer><script> + mytop = 0.13 * g_height; myleft = 0.09 * g_width; myheight = 0.8 * g_height; mywidth = 0.8 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.09 * g_width; +yy = 0.13 * g_height; +ht = 0.8 * g_height; +wd = 0.8 * g_width; +document.write( +'<img border=0 src="slide0009_image015.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Many of the data types in the previous slide are hot-linked and it is easy to generate a small web of correlations between any transcript of interest and many other transcripts. In this case, we have used green lines between transcripts that have positive correlations, and red lines between transcripts that have negative correlations. Correlations have been multiplied by 100. The correlation of 0.96 between App and Hsp84-1 reads 96.<span style="mso-spacerun: yes"> </span>These are Pearson product moment correlations and they are sensitive to outliers. If you prefer, you can recompute Spearman rank order correlations.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Where did Ndr4 (lower left) come from? It is not in the list in the previous slide. Actually it is. Nomenclature changes rapidly. If you click on R74996 in the previous slide (the active webqtl version) you will see that it now has a new symbol and name.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>What are all of the<span style="mso-spacerun: yes"> </span>conventions in this correlation network sketch.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Times size=3>1.</font><font face=Helvetica size=3>The official gene symbol = App</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. OUr estimate of the location of these gene in the Mouse Genome Sequencing Consoritum version 3 build (MGSCv3). Chromosome followed by the megabase position relative to the centromere. (Mice only have one chromosome arm so this is an unambiguous coordinate. )</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. The pair of numbers: top is the highest expression among the strain set. The lower number is the lowest expression of that transcript among the strain set.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>4. Vertical number on the right side of each box: this is the probe set ID given by Affymetrix. We have truncated these probe set IDs so you will not see the usual<span style="mso-spacerun: yes"> </span>ÒatÓ. A single gene may be represented by more than 10 probe sets. Thus this ID number is essential to identify the actual data source.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>5. Lower right corner: a two digit number followed by plus and minus signs. These numbers are the correlation value (absolute value) of the 100th best correlated transcript. The plus and minus signs indicate the mean polarity of the correlations.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>6. The set of numbers that read 2@140* etc. These are the approximate locations of additive effect QTLs detected by WebQTL that we will describe in other slides. Read this as: App has a suggestive QTL on Chr 2 at about 140 Mb and the D allele inherited from DBA/2J confirms a higher expression level at this marker.<span style="mso-spacerun: yes"> </span>If there is no star symbol, then it is not even formally ÒsuggestiveÓ but does make an interesting looking blip on the QTL radar screen.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0042.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0042.htm new file mode 100755 index 00000000..9cc37896 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0042.htm @@ -0,0 +1,102 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0042.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.01 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 1.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.12 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";mso-margin-left-alt:348; mso-text-indent-alt:56'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>What a network is likely to look like (but </span><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'> </span></span></layer><script> + mytop = 0.04 * g_height; myleft = 0.05 * g_width; myheight = 0.07 * g_height; mywidth = 0.85 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>will not be center of universe).</span></span></layer></div> </layer></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0.06 * g_width; myheight = 0.82 * g_height; mywidth = 0.71 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.06 * g_width; +yy = 0.15 * g_height; +ht = 0.82 * g_height; +wd = 0.71 * g_width; +document.write( +'<img border=0 src="slide0010_image016.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.32 * g_height; myleft = 0.45 * g_width; myheight = 0.03 * g_height; mywidth = 0.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-size:133%;color:#FF0F0F'><b><i>App</i></b></span></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>What networks are likely to really look like. This slide is taken from Lumeta Inc.<span style="mso-spacerun: yes"> </span>(www.lumeta.com). It actually illustrates the structure of connections across the<span style="mso-spacerun: yes"> </span>Internet. The large green area is a major Internet provider (WorldCom before the fall?).<span style="mso-spacerun: yes"> </span>Check<span style="mso-spacerun: yes"> </span>out Lumeta to see some more lovely graphs of this sort. Most biologists are familiar with simple sketches, but this is what we will have to be prepared to contend with soon.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0043.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0043.htm new file mode 100755 index 00000000..e0be795e --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0043.htm @@ -0,0 +1,112 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Are there experimental results to corroborate a link between App with Hsp84-1?"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0043.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0.02 * g_width; myheight = 0.21 * g_height; mywidth = 0.97 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.12 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt:232; mso-text-indent-alt:0;mso-line-spacing:" 0 ";mso-margin-left-alt:232; mso-text-indent-alt:0'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:68%'><i>Are there experimental results to corroborate a link </i></span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0.04 * g_width; myheight = 0.06 * g_height; mywidth = 0.87 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:68%'><i>between App with Hsp84-1?</i></span></span></layer></div> </layer></div> </layer><script> + mytop = 0.82 * g_height; myleft = 0.04 * g_width; myheight = 0.18 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div></div> </layer><script> + mytop = 0.29 * g_height; myleft = 0.04 * g_width; myheight = 0.13 * g_height; mywidth = 0.99 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.99 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:250%; color:#E9EB5D'><i>Yes: Heat shock 84-1 induces the expression of App, </i></span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.84 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:250%; color:#E9EB5D'><i>ubiquitin, and pyruvate kinase</i></span></span></layer></div> </layer><script> + mytop = 0.5 * g_height; myleft = 0.05 * g_width; myheight = 0.19 * g_height; mywidth = 0.95 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.95 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:250%; color:#E9EB5D'><i>Having ÒconfirmedÓ these known relations, we can </i></span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:250%; color:#E9EB5D'><i>now add new members to this family: Atp6l, Gnas, </i></span></span></layer><script> + mytop = 0.13 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.84 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:250%; color:#E9EB5D'><i>Ndr4. A thin veneer of functional genomics.</i></span></span></layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Having worked with WebQTL now for 30 minutes, do we know anything new? The hypothesis that we have generated (but not validated) is that three transcripts: Atp6l, Gnas, and Ndr4 are part of a family of genes that are coregulated in normal mouse forebrain with App and Hsp84-1. We need to add functional and mechanistic significance to this hypothesis to make it biologically vibrant. But from a statiistical standpoint it is a strong inference.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Please donÕt say: But these are mere correlations. A high correlation in this context has a biological basis. The real question is are we smart enough to understand the web (not chain) of causality that produced the correlation. Once we understand the web of causality, does it have utility? Very often the answer will be NO. This will often be the case when a high correlation is generated by linkage disequilibrium of sets of polymorphisms that modulate a set of mechanistically separated traits. Chromosomal linkage can produce correlations that are not mechanistic in the conventional sense used by molecular biologists. For example, clusters<span style="mso-spacerun: yes"> </span>of hox transcription factor genes tend to be close physically to keratin gene clusters, and one might expect shared patterns of variance produced by this linkage in a mapping panel, no matter how large.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>If Affymetrix designed probe sets with reasonable care, if we did the experiments correctly, if we sampled animals appropriately, then a correlation of 0.70 or higher between transcripts in the brain tells you that these two transcripts are effectively coupled in this set of animals under this set of conditions. More than 50% the variance in the expression of one transcript can be predicted from the other. That is a major piece of information that could be of significant clinical, economic, and predictive value, whatever its causes. Yes, correlation coefficients are noisy and have large error terms, but we have larger n of strains coming to the rescue. Expect more than 50 BXD lines soon.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>This is a thin veneer of functional genomics. It is enough to generate some marvelous hypotheses in a semi-automated way.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0044.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0044.htm new file mode 100755 index 00000000..06443316 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0044.htm @@ -0,0 +1,107 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0044.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.01 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt: 292;mso-text-indent-alt:0;mso-line-spacing:" 0 ";mso-margin-left-alt:292; mso-text-indent-alt:0'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>2.45 billion scatter plots: </span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>here is one of the best</span></div> </layer></div> </layer><script> + mytop = 0.11 * g_height; myleft = 0.06 * g_width; myheight = 0.82 * g_height; mywidth = 0.67 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.06 * g_width; +yy = 0.11 * g_height; +ht = 0.82 * g_height; +wd = 0.67 * g_width; +document.write( +'<img border=0 src="slide0012_image017.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.77 * g_height; myleft = 0.41 * g_width; myheight = 0.07 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:283%; color:#003399;mso-color-index:4'><i>App</i></span><span style='font-family: "Gill Sans";font-size:283%;color:#E9EB5D;mso-color-index:3;mso-special-format: lastCR;display:none'><i><br> </i></span></div> </layer><script> + mytop = 0.36 * g_height; myleft = 0.14 * g_width; myheight = 0.27 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.14 * g_width; +yy = 0.36 * g_height; +ht = 0.27 * g_height; +wd = 0.06 * g_width; +document.write( +'<img border=0 src="slide0012_image018.gif" alt="Text Box: Hsp84-1" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The correlation between App and heat shock protein 84-1 transcript is most impressive.<span style="mso-spacerun: yes"> </span>Since WebQTL now contains total of about 70,000 traits in the BXD strains, we could produce as many as to 70k x 35k scatter plots of this type. Since all of the<span style="mso-spacerun: yes"> </span>correlations come for a common reference population, none<span style="mso-spacerun: yes"> </span>of the correlations are blantantly silly. However the great majority may be uninterpretable and a very large number may be meaningless given the signal-to-noise ratios of some measurements. With about 30 strains, correlations above 0.7 have a reasonably low false positive rate.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0045.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0045.htm new file mode 100755 index 00000000..d3c4b2af --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0045.htm @@ -0,0 +1,104 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0045.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; 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+</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.01 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.9 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";mso-margin-left-alt:348; mso-text-indent-alt:56'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Cross-tissue type correlations</span></div> </layer></div> </layer><script> + mytop = 0.11 * g_height; myleft = 0.04 * g_width; myheight = 0.46 * g_height; mywidth = 0.71 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.04 * g_width; +yy = 0.11 * g_height; +ht = 0.46 * g_height; +wd = 0.71 * g_width; +document.write( +'<img border=0 src="slide0013_image019.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.6 * g_height; myleft = 0.04 * g_width; myheight = 0.35 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.04 * g_width; +yy = 0.6 * g_height; +ht = 0.35 * g_height; +wd = 0.89 * g_width; +document.write( +'<img border=0 src="slide0013_image020.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>We can compare App expression inthe forebrain against transcript expression in hematopoietic stem cells. Some of these correlations are significant, but it may be difficult to discovery of shared genetic (linkage disequilibrium) or molecular processes that give rise to these correlation.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The GNF Hematopoietic stem cell data belong to Gerald de Haan (University of Groningen) and Michael Cooke (Genomics Institute of the Novartis Research Foundation).</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0046.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0046.htm new file mode 100755 index 00000000..77bd0a8b --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0046.htm @@ -0,0 +1,110 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0046.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.01 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 1.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.12 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";mso-margin-left-alt:348; mso-text-indent-alt:56'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Cross-modal correlations: From mRNA to to </span></span></layer><script> + mytop = 0.04 * g_height; myleft = 0.05 * g_width; myheight = 0.07 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>anatomy and to behavior and pharmacology</span></span></layer></div> </layer></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0.06 * g_width; myheight = 0.34 * g_height; mywidth = 0.53 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.06 * g_width; +yy = 0.15 * g_height; +ht = 0.34 * g_height; +wd = 0.53 * g_width; +document.write( +'<img border=0 src="slide0014_image021.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.46 * g_height; myleft = 0.17 * g_width; myheight = 0.53 * g_height; mywidth = 0.65 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.17 * g_width; +yy = 0.46 * g_height; +ht = 0.53 * g_height; +wd = 0.65 * g_width; +document.write( +'<img border=0 src="slide0014_image022.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Another example, but in this case we are generating correlations between variation in transcript levels with a database of approximately 430 published (and unpublished) phenotypes from BXD strains. Notice that the N of strains is variable (from 21 to 28 above). Rank order statistics is more appropriate when N is under 30.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The Published Phenotypes database was prepared by Elissa Chesler and Robert Williams from data extracted from the literature or sent to us for inclusion by our colleagues. We especially thank John Crabbe (Oregon HSU) and Byron Jones (Pennsylvania SU) for providing us with large pre-compiled data tables.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0047.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0047.htm new file mode 100755 index 00000000..9f73a171 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0047.htm @@ -0,0 +1,155 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: WebQTL link to www.webqtl.org/search.html"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0047.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0.02 * g_width; myheight = 0.19 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.19 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt:232; mso-text-indent-alt:0;mso-line-spacing:" 0 ";mso-margin-left-alt:232; mso-text-indent-alt:0'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:68%'><i>WebQTL<span style="mso-spacerun: yes"> </span><br> </i></span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0.04 * g_width; myheight = 0.06 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:68%'><i>link to <br> </i></span></span></layer><script> + mytop = 0.11 * g_height; myleft = 0.04 * g_width; myheight = 0.08 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:86%'><i>www.webqtl.org/search.html</i></span><span style='font-size:68%;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </layer><script> + mytop = 0.36 * g_height; myleft = 0.02 * g_width; myheight = 0.45 * g_height; mywidth = 0.73 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.36 * g_height; mywidth = 0.71 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.67 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> + mytop = 0 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.62 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'><span style='mso-special-format:numbullet;color:#FBFDB8;position:absolute; left:-8.06%;font-family:Times;font-size:99%'>1.</span></span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Discovering shared expression </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.55 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>patterns<br> </span></span></layer></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.6 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> + mytop = 0 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.55 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'><span style='mso-special-format:numbullet;color:#FBFDB8;position:absolute; left:-9.09%;font-family:Times;font-size:99%'>2.</span></span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Discovering upstream </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.55 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>modulators (QTLs)<br> </span></span></layer></div> </layer><script> + mytop = 0.3 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.71 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> + mytop = 0 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.66 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'><span style='mso-special-format:numbullet;color:#FBFDB8;position:absolute; left:-7.61%;font-family:Times;font-size:99%'>3.</span></span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Discovering downstream targets</span></span></layer></div> </layer></div> </layer></div> </layer><script> + mytop = 0.17 * g_height; 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myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:"Arial Rounded MT Bold";font-size:233%;color:#6E6E6E'>RNA</span><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; display:none'><br> </span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.82 * g_height; myleft = 0.04 * g_width; myheight = 0.18 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div></div> </layer><script> + mytop = 0.51 * g_height; myleft = 0.47 * g_width; myheight = 0.1 * g_height; mywidth = 0.26 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.47 * g_width; +yy = 0.51 * g_height; +ht = 0.1 * g_height; +wd = 0.26 * g_width; +document.write( +'<img border=0 src="slide0015_image024.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Part 2: Mapping upstream modulators or QTLs. A quantitative trait locus is a chromosomal region that harbors one or a few polymorphic gene loci that influence a trait. We are going to be looking for QTLs that modulate the steady state expression level of App in the adult mouse forebrain.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0048.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0048.htm new file mode 100755 index 00000000..53a7011d --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0048.htm @@ -0,0 +1,897 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; 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+</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master05_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.92 * g_height; myleft = 0.08 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.02 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Times;font-size:117%;color:white;display:none'><br> </span></div> </layer><script> + mytop = 0.03 * g_height; 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mywidth = 0.29 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Times;font-size:117%; color:white;display:none'><br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.02 * g_height; mywidth = 0.29 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Times;font-size:117%; color:white;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.02 * g_height; myleft = -0.02 * g_width; myheight = 0.11 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.09 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"%0 0 0";mso-margin-left-alt: 16;mso-text-indent-alt:16'><span style='font-family:Arial;font-size:267%; color:#E9EB5D'><i>How to make recombinant inbred strains (RI)</i></span><span style='font-family:Arial;font-size:150%;color:aqua;display:none'><br> </span></div> </layer><script> + mytop = 0.06 * g_height; 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myleft = 0.28 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.28 * g_width; +yy = 0.2 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0016_image026.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0.25 * g_width; myheight = 0.1 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>C57BL/6J (B)<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.3 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.3 * g_width; +yy = 0.2 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0016_image027.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0.62 * g_width; myheight = 0.1 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>DBA/2J (D)<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.66 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.66 * g_width; +yy = 0.2 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0016_image028.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.23 * g_width; myheight = 0.01 * g_height; mywidth = 0.5 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.23 * g_width; +yy = 0.35 * g_height; +ht = 0.01 * g_height; +wd = 0.5 * g_width; +document.write( +'<img border=0 src="slide0016_image029.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.24 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.24 * g_width; +yy = 0.35 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0016_image030.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.4 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.4 * g_width; +yy = 0.35 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0016_image031.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.57 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.57 * g_width; +yy = 0.35 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0016_image032.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.74 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.74 * g_width; +yy = 0.35 * g_height; +ht = 0.03 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0016_image033.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.42 * g_height; myleft = 0.05 * g_width; myheight = 0.12 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F1<br> </b></span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format: lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.39 * g_height; myleft = 0.22 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.22 * g_width; +yy = 0.39 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0016_image034.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.39 * g_height; myleft = 0.38 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.38 * g_width; +yy = 0.39 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0016_image035.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.39 * g_height; myleft = 0.55 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.55 * g_width; +yy = 0.39 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0016_image036.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.39 * g_height; myleft = 0.72 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.72 * g_width; +yy = 0.39 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0016_image037.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.43 * g_height; myleft = 0.43 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.43 * g_width; +yy = 0.43 * g_height; +ht = 0.03 * g_height; +wd = 0.11 * g_width; +document.write( +'<img border=0 src="slide0016_image038.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.6 * g_height; myleft = 0.2 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.2 * g_width; +yy = 0.6 * g_height; +ht = 0.03 * g_height; +wd = 0.09 * g_width; +document.write( +'<img border=0 src="slide0016_image039.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.71 * g_height; myleft = 0.58 * g_width; myheight = 0.27 * g_height; mywidth = 0.2 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.03 * g_height; myleft = 0.01 * g_width; myheight = 0.22 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.15 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:117%; color:#FFFF99'><b>20 generations </b></span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:117%; color:#FFFF99'><b>brother-sister </b></span></span></layer><script> + mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:117%; color:#FFFF99'><b>matings</b></span><span style='font-family:Arial;font-size: 233%;color:#FFFF99;display:none'><b><br> </b></span></span></layer></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Arial;font-size:233%; color:#FFFF99;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.6 * g_height; myleft = 0.5 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.5 * g_width; +yy = 0.6 * g_height; +ht = 0.03 * g_height; +wd = 0.09 * g_width; +document.write( +'<img border=0 src="slide0016_image040.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.62 * g_height; myleft = 0.54 * g_width; myheight = 0.28 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.54 * g_width; +yy = 0.62 * g_height; +ht = 0.28 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0016_image041.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.61 * g_height; myleft = 0.79 * g_width; myheight = 0.03 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.79 * g_width; +yy = 0.61 * g_height; +ht = 0.03 * g_height; +wd = 0.1 * g_width; +document.write( +'<img border=0 src="slide0016_image042.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.62 * g_height; myleft = 0.83 * g_width; myheight = 0.28 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.83 * g_width; +yy = 0.62 * g_height; +ht = 0.28 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0016_image043.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.92 * g_height; myleft = 0.21 * g_width; myheight = 0.1 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD1</span><span style='font-family:Arial;font-size:150%;color:#484848;display:none'><br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#484848;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.92 * g_height; myleft = 0.51 * g_width; myheight = 0.1 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD2<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.92 * g_height; myleft = 0.8 * g_width; myheight = 0.06 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>BXD80</span></div> </layer></div> </layer><script> + mytop = 0.9 * g_height; myleft = 0.64 * g_width; myheight = 0.17 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.15 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:300%;color:#FFFF99'>+ É +<br> </span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:300%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.62 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F2<br> </b></span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format: lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.18 * g_width; myheight = 0.01 * g_height; mywidth = 0.75 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.18 * g_width; +yy = 0.54 * g_height; +ht = 0.01 * g_height; +wd = 0.75 * g_width; +document.write( +'<img border=0 src="slide0016_image044.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.17 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.17 * g_width; +yy = 0.54 * g_height; +ht = 0.03 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0016_image045.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.32 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.32 * g_width; +yy = 0.54 * g_height; +ht = 0.03 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0016_image046.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.48 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.48 * g_width; +yy = 0.54 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0016_image047.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.62 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.62 * g_width; +yy = 0.54 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0016_image048.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.77 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.77 * g_width; +yy = 0.54 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0016_image049.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.92 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.92 * g_width; +yy = 0.54 * g_height; +ht = 0.03 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0016_image050.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.44 * g_height; myleft = 0.49 * g_width; myheight = 0.1 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.49 * g_width; +yy = 0.44 * g_height; +ht = 0.1 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0016_image051.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.15 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.15 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0016_image052.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.3 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.3 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0016_image053.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.46 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.46 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0016_image054.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.6 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.6 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0016_image055.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.75 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.75 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0016_image056.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.9 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.9 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0016_image057.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.84 * g_height; myleft = 0.56 * g_width; myheight = 0.01 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.56 * g_width; +yy = 0.84 * g_height; +ht = 0.01 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0016_image058.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.8 * g_height; myleft = 0.25 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.25 * g_width; +yy = 0.8 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0016_image059.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.84 * g_height; myleft = 0.86 * g_width; myheight = 0.02 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.86 * g_width; +yy = 0.84 * g_height; +ht = 0.02 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0016_image060.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.75 * g_height; myleft = 0.01 * g_width; myheight = 0.14 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'><b>BXD RI<br> </b></span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'><b>Strain set<br> </b></span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.01 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.12 * g_height; myleft = 0.14 * g_width; myheight = 0.06 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.14 * g_width; +yy = 0.12 * g_height; +ht = 0.06 * g_height; +wd = 0.1 * g_width; +document.write( +'<img border=0 src="slide0016_image061.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.76 * g_width; myheight = 0.08 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.76 * g_width; +yy = 0.1 * g_height; +ht = 0.08 * g_height; +wd = 0.14 * g_width; +document.write( +'<img border=0 src="slide0016_image062.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.17 * g_width; myheight = 0.14 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>fully<br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>inbred<br> </span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.38 * g_height; myleft = 0.02 * g_width; myheight = 0.1 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>isogenic<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.01 * g_width; myheight = 0.14 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>hetero-<br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>geneous<br> </span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.74 * g_height; myleft = 0.29 * g_width; myheight = 0.22 * g_height; mywidth = 0.22 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.19 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.15 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>Recombined </span></span></layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>chromosomes </span></span></layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>are needed for </span></span></layer><script> + mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>mapping<br> </span></span></layer></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.25 * g_width; myheight = 0.1 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>female<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.64 * g_width; myheight = 0.1 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>male<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.3 * g_height; myleft = 0.78 * g_width; myheight = 0.1 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:117%;color:#FFFF99'>chromosome pair</span><span style='font-family:Arial;font-size:150%;color:#FFFF99; display:none'><br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.31 * g_height; myleft = 0.65 * g_width; myheight = 0.02 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.65 * g_width; +yy = 0.31 * g_height; +ht = 0.02 * g_height; +wd = 0.12 * g_width; +document.write( +'<img border=0 src="slide0016_image063.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.86 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.12 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%; color:#E9EB5D'>Inbred<br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%; color:#E9EB5D'>Isogenic<br> </span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%; color:#E9EB5D'>siblings</span><span style='font-family:Arial;font-size:117%; color:aqua;display:none'><br> </span></div> </layer><script> + mytop = 0.09 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%; color:aqua;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.79 * g_height; myleft = 0.83 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.83 * g_width; +yy = 0.79 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0016_image064.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.79 * g_height; myleft = 0.53 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.53 * g_width; +yy = 0.79 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0016_image065.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.8 * g_height; myleft = 0.23 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.23 * g_width; +yy = 0.8 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0016_image066.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.18 * g_height; myleft = 0.43 * g_width; myheight = 0.09 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:300%;color:aqua'>B</span><span style='font-family:Arial;font-size:300%;color:#FFFF99'>X</span><span style='font-family:Arial;font-size:300%;color:#FF1911'>D</span></div> </layer></div> </layer><script> + mytop = 0.27 * g_height; myleft = 0.32 * g_width; myheight = 0.04 * g_height; mywidth = 0.31 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.32 * g_width; +yy = 0.27 * g_height; +ht = 0.04 * g_height; +wd = 0.31 * g_width; +document.write( +'<img border=0 src="slide0016_image067.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.66 * g_height; myleft = 0.6 * g_width; myheight = 0.03 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.6 * g_width; +yy = 0.66 * g_height; +ht = 0.03 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0016_image068.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.64 * g_height; myleft = 0.15 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.15 * g_width; +yy = 0.64 * g_height; +ht = 0.05 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0016_image069.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.75 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.75 * g_width; +yy = 0.57 * g_height; +ht = 0.05 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0016_image070.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.28 * g_height; myleft = 0.48 * g_width; myheight = 0.08 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.48 * g_width; +yy = 0.28 * g_height; +ht = 0.08 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0016_image071.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.62 * g_height; myleft = 0.23 * g_width; myheight = 0.16 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.23 * g_width; +yy = 0.62 * g_height; +ht = 0.16 * g_height; +wd = 0.03 * g_width; +document.write( +'<img border=0 src="slide0016_image072.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.61 * g_height; myleft = 0.63 * g_width; myheight = 0.08 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.63 * g_width; +yy = 0.61 * g_height; +ht = 0.08 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0016_image073.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The next set of slides provide a very short interlude on QTL mapping. You will need to do some independent reading on this topic if this is your first exposure to QTL mapping. The recombinant inbred strains that we are using in WebQTL and in this particular demo were generated about 25 years ago by Dr. Ben Taylor at The Jackson Laboratory. He crossed a female C57BL/6J mouse with a male DBA/2J mice. At the bottom of this slide we have schematized one chromosome pair from three out of 80 BXD RI strains.<span style="mso-spacerun: yes"> </span>The dashed vertical lines that lead to the final BXD RI lines involve 20 full sib matings (about 6 years of breeding). Some lines die<span style="mso-spacerun: yes"> </span>out during inbreeding. For example, there is no extant BXD3 or BXD4 strain.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0049.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0049.htm new file mode 100755 index 00000000..54040ab2 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0049.htm @@ -0,0 +1,427 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0049.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; 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+</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.4 * g_height; myleft = 0.73 * g_width; myheight = 0.05 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.73 * g_width; +yy = 0.4 * g_height; +ht = 0.05 * g_height; +wd = 0.14 * g_width; +document.write( +'<img border=0 src="slide0017_image074.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.4 * g_height; myleft = 0.74 * g_width; myheight = 0.07 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Gadget;font-size:150%;color:white'>aa<br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Gadget;font-size:150%;color:white;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0.73 * g_width; myheight = 0.05 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.73 * g_width; +yy = 0.16 * g_height; +ht = 0.05 * g_height; +wd = 0.14 * g_width; +document.write( +'<img border=0 src="slide0017_image075.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0.74 * g_width; myheight = 0.07 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Gadget;font-size:150%;color:white'>aaaa<br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Gadget;font-size:150%;color:white;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.71 * g_width; myheight = 0.19 * g_height; mywidth = 0.25 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.24 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.24 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:267%;color:#E2EBF0'>D2 strain</span><span style='font-family:Palatino;font-size:333%;color:#FBFDB8;display:none'><br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-family:Palatino;font-size:333%;color:#FBFDB8;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.43 * g_height; myleft = 0.71 * g_width; myheight = 0.19 * g_height; mywidth = 0.25 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.02 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.24 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.24 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:267%;color:#F6BF69'>B6 strain</span><span style='font-family:Palatino;font-size:333%;color:#F6BF69;display:none'><br> </span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-family:Palatino;font-size:333%;color:#F6BF69;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.17 * g_height; myleft = 0.31 * g_width; myheight = 0.42 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.31 * g_width; +yy = 0.17 * g_height; +ht = 0.42 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0017_image076.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.4 * g_height; myleft = 0.31 * g_width; myheight = 0.03 * g_height; mywidth = 0.39 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.31 * g_width; +yy = 0.4 * g_height; +ht = 0.03 * g_height; +wd = 0.39 * g_width; +document.write( +'<img border=0 src="slide0017_image077.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.17 * g_height; myleft = 0.4 * g_width; myheight = 0.31 * g_height; mywidth = 0.3 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.03 * g_height; myleft = 0.01 * g_width; myheight = 0.26 * g_height; mywidth = 0.27 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.16 * g_height; mywidth = 0.27 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.27 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'><i>amount of </i></span></span></layer><script> + mytop = 0.09 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.27 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'><i>transcript</i></span><span style='font-family:Palatino;font-size:367%;color:#E9EB5D;display:none'><br> </span></span></layer></div> </layer><script> + mytop = 0.17 * g_height; myleft = 0 * g_width; myheight = 0.09 * g_height; mywidth = 0.27 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-family:Palatino;font-size:367%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0.72 * g_width; myheight = 0.19 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:267%;color:white'>4 </span><span style='font-size: 233%;color:white'>units</span><span style='font-family:Palatino;font-size:333%; color:#E9EB5D;display:none'><br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-family:Palatino;font-size:333%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.29 * g_height; myleft = 0.72 * g_width; myheight = 0.19 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.02 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:267%;color:white'>2</span><span style='font-size: 233%;color:white'> units</span><span style='font-family:Palatino;font-size: 333%;color:#E9EB5D;display:none'><br> </span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-family:Palatino;font-size:333%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0.31 * g_width; myheight = 0.05 * g_height; mywidth = 0.4 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.31 * g_width; +yy = 0.15 * g_height; +ht = 0.05 * g_height; +wd = 0.4 * g_width; +document.write( +'<img border=0 src="slide0017_image078.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.17 * g_height; myleft = 0.09 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#E2EBF0'>D<br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.17 * g_height; myleft = 0.17 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69'>B<br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.77 * g_height; myleft = 0.05 * g_width; myheight = 0.26 * g_height; mywidth = 1.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.02 * g_height; myleft = 0.01 * g_width; myheight = 0.22 * g_height; mywidth = 1.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.14 * g_height; mywidth = 1.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E2EBF0'>D</span><span style='font-size:233%;color:#E9EB5D'> </span><span style='font-size:200%; color:#E9EB5D'>and </span><span style='font-size:233%;color:#F6BF69'>B</span><span style='font-size:233%;color:#E9EB5D'> </span><span style='font-size:200%; color:#E9EB5D'>may be SNP-like variants in the promoter </span></span></layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:200%;color:#E9EB5D'>itself (cis QTL) or in </span><span style='font-size:200%;color:#EAEC5E'>upstream genes (trans QTLs)</span><span style='font-size:300%;color:#E9EB5D;display:none'><br> </span></span></layer></div> </layer><script> + mytop = 0.14 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#E9EB5D;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.04 * g_width; myheight = 0.16 * g_height; mywidth = 0.22 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.22 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-size:200%;color:#E9EB5D'>UPSTREAM<br> </span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.22 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-size:200%;color:#E9EB5D'>modulators<br> </span></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.01 * g_width; myheight = 0.05 * g_height; mywidth = 0.2 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-size:200%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.44 * g_width; myheight = 0.18 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:300%;color:#E2EBF0'>High<br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.63 * g_height; myleft = 0.08 * g_width; myheight = 0.18 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#E2EBF0'>D<br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.63 * g_height; myleft = 0.15 * g_width; myheight = 0.18 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69'>B<br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.71 * g_height; myleft = 0.07 * g_width; myheight = 0.12 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D'><i>cis QTL</i></span><span style='font-size:200%;color:#E9EB5D;display:none'><br> </span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.57 * g_height; myleft = -0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = -0.01 * g_width; +yy = 0.57 * g_height; +ht = 0.07 * g_height; +wd = 1.01 * g_width; +document.write( +'<img border=0 src="slide0017_image079.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.44 * g_height; myleft = 0.47 * g_width; myheight = 0.12 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:233%;color:#F6BF69'>Low<br> </span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:233%;color:#F6BF69;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.58 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.04 * g_height; mywidth = 1.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:17'><span style='font-family:Gadget;font-size:167%;color:white'>>>>>PROMOTER--ATG-Exon1-Intron1-Exon2-Intron2 - etc-3'UTR >>>>></span></div> </layer></div> </layer><script> + mytop = 0.37 * g_height; myleft = 0.08 * g_width; myheight = 0.2 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.08 * g_width; +yy = 0.37 * g_height; +ht = 0.2 * g_height; +wd = 0.13 * g_width; +document.write( +'<img border=0 src="slide0017_image080.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.39 * g_height; myleft = 0.1 * g_width; myheight = 0.12 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white'><b><br> </b></span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> + mytop = 0.4 * g_height; myleft = 0.17 * g_width; myheight = 0.12 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white'><b><br> </b></span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> + mytop = 0.33 * g_height; myleft = 0.08 * g_width; myheight = 0.2 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.08 * g_width; +yy = 0.33 * g_height; +ht = 0.2 * g_height; +wd = 0.13 * g_width; +document.write( +'<img border=0 src="slide0017_image081.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.17 * g_width; myheight = 0.12 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white'><b><br> </b></span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.1 * g_width; myheight = 0.12 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white'><b><br> </b></span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> + mytop = 0.37 * g_height; myleft = 0.2 * g_width; myheight = 0.12 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;display:none'><b><br> </b></span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> + mytop = 0.27 * g_height; myleft = 0.04 * g_width; myheight = 0.21 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.04 * g_width; +yy = 0.27 * g_height; +ht = 0.21 * g_height; +wd = 0.21 * g_width; +document.write( +'<img border=0 src="slide0017_image082.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.27 * g_height; myleft = 0.05 * g_width; myheight = 0.12 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D'><i>trans QTL</i></span><span style='font-size:200%;color:#E9EB5D;display:none'><br> </span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>This slide is illustrates two categories of QTLs that modulate variability in transcript abundance.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. cis QTLs are defined as QTLs that are closely linked to the gene whose transcript is the measured trait. For example, a polymorphism in the promoter that affects the binding of a transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms in enhancers. They may also be polymorphisms in neigghboring genes.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. trans QTLs map far enough away from the location of the gene that gives rise to the transcript that is being measured so that we can be quite certain that the QTL is not IN the gene itself. The most blatant type of trans-QTL would be a polymorphism in a transcription factor. BUT in the majority of cases, the trans QTLs can be far removed in a mechanistic sense from the actual events modulating transcript abundance. That is why there are three overlappoing arrows above.<span style="mso-spacerun: yes"> </span>The way in which an upstream polymorphism influences a downstream difference in mRNA abundance can be very indirect. Effects can :</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>a.<span style="mso-spacerun: yes"> </span>cross tissue types (a polymorphic liver enzyme may affect CNS gene expression)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>b.<span style="mso-spacerun: yes"> </span>cross time (the modulator is only expressed for one day during development but has permanent effects in adults),</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>c.<span style="mso-spacerun: yes"> </span>may be contingent on environmental factors (heat shock may trigger the expression of a polymorphic factor that affects mRNA abundance).</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0050.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0050.htm new file mode 100755 index 00000000..3c2f20c7 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0050.htm @@ -0,0 +1,107 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: WebQTL to exploring upstream control"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0050.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.02 * g_height; myleft = 0.04 * g_width; myheight = 0.09 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-line-spacing:" 0 "'><span style='font-family:Verdana;font-size:73%'><i>WebQTL to exploring upstream control</i></span></div> </layer></div> </layer><script> + mytop = 0.13 * g_height; myleft = 0.05 * g_width; myheight = 0.62 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.05 * g_width; +yy = 0.13 * g_height; +ht = 0.62 * g_height; +wd = 0.89 * g_width; +document.write( +'<img border=0 src="slide0018_image083.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.19 * g_height; myleft = 0.55 * g_width; myheight = 0.25 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.55 * g_width; +yy = 0.19 * g_height; +ht = 0.25 * g_height; +wd = 0.19 * g_width; +document.write( +'<img border=0 src="slide0018_image084.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0.74 * g_width; myheight = 0.05 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:217%; color:#FF0F0F'>Just click</span></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Back to the demo. Please bring the Traiit Data and Editing window to the front and look for the Interval Mapping button. Please confirm that you are back to the trait amyloid beta precursor protein.<span style="mso-spacerun: yes"> </span>If so, then just click the button.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notice that the default for:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Select Chrs (chromosomes) is ALL</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Select Probes is Probe Set</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Options: Permuation test YES<span style="mso-spacerun: yes"> </span>(1000 is the default number)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Options: Bootstrap test YES (1000 is the default number)</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0051.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0051.htm new file mode 100755 index 00000000..39d20b2b --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0051.htm @@ -0,0 +1,127 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: WebQTL to exploring upstream control."> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0051.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; 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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.02 * g_height; myleft = 0.04 * g_width; myheight = 0.09 * g_height; mywidth = 1.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt:233; mso-text-indent-alt:0;mso-line-spacing:" 0 ";mso-margin-left-alt:233; mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:73%'><i>WebQTL to exploring upstream control.</i></span></div> </layer></div> </layer><script> + mytop = 0.27 * g_height; myleft = 0.01 * g_width; myheight = 0.51 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.27 * g_height; +ht = 0.51 * g_height; +wd = 0.96 * g_width; +document.write( +'<img border=0 src="slide0019_image085.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.13 * g_height; myleft = 0.19 * g_width; myheight = 0.06 * g_height; mywidth = 0.6 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-size:233%;color:#E9EB5D'><i>App maps on Chr 16 here</i></span></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0.68 * g_width; myheight = 0.37 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.68 * g_width; +yy = 0.15 * g_height; +ht = 0.37 * g_height; +wd = 0.14 * g_width; +document.write( +'<img border=0 src="slide0019_image086.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.53 * g_height; myleft = 0.13 * g_width; myheight = 0.37 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.13 * g_width; +yy = 0.53 * g_height; +ht = 0.37 * g_height; +wd = 0.14 * g_width; +document.write( +'<img border=0 src="slide0019_image087.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.82 * g_height; myleft = 0.26 * g_width; myheight = 0.14 * g_height; mywidth = 0.9 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.75 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-size:267%;color:#E9EB5D'><i>Is App modulated by Chr 2?<br> </i></span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.9 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-size:267%;color:#E9EB5D'><i>Probably, but donÕt bet the farm. </i></span></div> </layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>This is the main output type: a so-called full genome interval map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The X-axis represents all 19 autosomes and the X chromosome as if they were laid end to end with short gaps between the telomere of one chromosome and the centromere of the next chromosome (mouse chromsomes only have a single long arm and the centromere represents the origin of each chromosome for numerical purpose: 0 centimorgans and almost 0 megabases). The blue labels along the bottom of the figure list a subset of markers that were used in mapping. We used 753 markers to perform the mapping but here we just list five markers per chromosome.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The thick blue wavy line running across chromsomes summarizes the strength of association between variation in the phenotype (App expression differences) and the two genotypes of 753 markers and the intervals between markers (hence, interval mapping).<span style="mso-spacerun: yes"> </span>The height of the wave (blue Y-axis to the left) provides the likelihood ratio statistic (LRS). Divide by 4.61 to convert these values to LOD scores.<span style="mso-spacerun: yes"> </span>Or you can read them as a chi-square-like statistic.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The red line and the red axis to the far right provides an estimate of the effect<span style="mso-spacerun: yes"> </span>that a QTL has on expression of App (this estimate of the addtive effect tends to be an overestimate). If the red line is below the X-axis then this means that the allele inherited from C57BL/6J (B6 or B) at a particular marker is associated with higher values. If the red line is above the X-axis then the DBA/2J allele (D2 or D) is associated with higher traits. Multiply the additive effect size by 2 to estimate the difference between the set of strains that have the B/B genotype and the D/D genotype at a specific marker. For example, on Chr 2 the red line<span style="mso-spacerun: yes"> </span>peaks at a value<span style="mso-spacerun: yes"> </span>of about 0.25. That means that this region of chromosome 2 is responsible for a 0.5 unit expression difference between B/B strains and the D/D strains. Since the units are log base 2, this is 2^0.5, or about a 41% difference in expression with the D/D group being high.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The yellow histogram bars: These summarize the results of a whole-genome bootstrap of the trait that is performed 1000 times. What is a bootstrap? A bootstrap provides you a metho of evaluating whether results are robust. If we drop out one strain, do we still get the same results? When mapping quantitative traits, each strain normally gets one equally weighted vote. But inthe bootstrap procedure, we give each strain a random weighting factor of between 0 and 1.<span style="mso-spacerun: yes"> </span>We then remap the trait and find THE SINGLE BEST LRS VALUE per bootstrap. We do this 1000 times. In this example, most bootstrap results cluster on Chr 2 under the LRS peak. That is somewhat reassuring. But notice that a substantial number of bootstrap results prefer Chr 7 or Chr 18.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The horizontal dashed lines at 9.6 and 15.9. These lines are the LRS values associated with the suggestive and significant false positive rates for genome-wide scans established by permuations of phenotypes across genotypes. We shuffle randomly 1000 times and obtain a distribution of peak LRS scores to generate a null distribution. Five percent of the time, one of these permuted data sets will have a peak LRS higher than 15.9. We call that level the 0.05 significance threshold for a whole genome scan. The p = 0.67 point is the the suggestive level, and corresponds to the green dashed line.<span style="mso-spacerun: yes"> </span>These thresholds are conservative for transcripts that have expression variation that is highly heritable. The putative or suggestive QTL on Chr 2 is probably more than just suggestive.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>One other point: the mapping procedure we use is computationally very fast, but it is relatively simple. We are not looking for gene-gene interactions and we are not fitting multiple QTLs in combinations.<span style="mso-spacerun: yes"> </span>Consider this QTL analysis a first pass that will highlight hot spots and warm spots that are worth following up on using more sophisticated models.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>CLICKABLE REGIONS:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. If you click on the Chromosome number then you will generate a new map just for that chromosome.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. If you click on the body of the map, say on the blue line, then you will generate a view<span style="mso-spacerun: yes"> </span>on a 10 Mb window of that part of the genome from the UCSC Genome Browser web site.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. If you click on a marker symbol, then you will generate a new Trait data and editing window with the genotypes loaded into the window just like any other trait. More on this later.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>NOTE: you can drag these maps off of the browser window and onto your desktop. The will be saved as PNG or PDF files. You can import them into Photoshop or other programs.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0052.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0052.htm new file mode 100755 index 00000000..54843d1c --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0052.htm @@ -0,0 +1,93 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: The whole neighborhood is modulated!"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0052.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.02 * g_height; myleft = 0.04 * g_width; myheight = 0.09 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-line-spacing:" 0 "'><span style='font-family:Verdana;font-size:73%'><i>The whole neighborhood is modulated!</i></span></div> </layer></div> </layer><script> + mytop = 0.13 * g_height; myleft = 0.09 * g_width; myheight = 0.8 * g_height; mywidth = 0.8 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.09 * g_width; +yy = 0.13 * g_height; +ht = 0.8 * g_height; +wd = 0.8 * g_width; +document.write( +'<img border=0 src="slide0020_image088.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>App has a suggestive QTL on Chr 2. What about the neighbors that we defined as having shared expression patterns. This figure shows that members of the immediate App neigborhood share a weak Chr 2 QTL.<span style="mso-spacerun: yes"> </span>That is what the blue oval in the background is meant to represent. But some transcripts, such as Ndr4 and Psen2 do not share this Chr 2 interval.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>QUESTION: What kind of headway can we make in detemining what polymorphism or polymorphisms on Chr 2 near 130 Mb might contribute to the variance in the expression of all of these important transcripts?</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0053.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0053.htm new file mode 100755 index 00000000..baaa7eee --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0053.htm @@ -0,0 +1,139 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Which gene is the QTL?"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0053.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.02 * g_height; myleft = 0.04 * g_width; myheight = 0.09 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-line-spacing:" 0 "'><span style='font-family:Verdana;font-size:73%'><i>Which gene is the QTL?</i></span></div> </layer></div> </layer><script> + mytop = 0.13 * g_height; myleft = 0.05 * g_width; myheight = 0.37 * g_height; mywidth = 0.58 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.05 * g_width; +yy = 0.13 * g_height; +ht = 0.37 * g_height; +wd = 0.58 * g_width; +document.write( +'<img border=0 src="slide0021_image089.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.46 * g_height; myleft = 0.03 * g_width; myheight = 0.51 * g_height; mywidth = 0.68 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.03 * g_width; +yy = 0.46 * g_height; +ht = 0.51 * g_height; +wd = 0.68 * g_width; +document.write( +'<img border=0 src="slide0021_image090.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.38 * g_height; myleft = 0.55 * g_width; myheight = 0.25 * g_height; mywidth = 0.24 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.55 * g_width; +yy = 0.38 * g_height; +ht = 0.25 * g_height; +wd = 0.24 * g_width; +document.write( +'<img border=0 src="slide0021_image091.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.75 * g_width; myheight = 0.28 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center'><span style='font-size:267%;color:#E9EB5D'><i>Right <br> </i></span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center'><span style='font-size:267%;color:#E9EB5D'><i>position<br> </i></span></div> </layer><script> + mytop = 0.14 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center'><span style='font-size:267%;color:#E9EB5D'><i>&<br> </i></span></div> </layer><script> + mytop = 0.21 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center'><span style='font-size:267%;color:#E9EB5D'><i>high r</i></span></div> </layer></div> </layer><script> + mytop = 0.5 * g_height; myleft = 0.72 * g_width; myheight = 0.14 * g_height; mywidth = 0.28 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.07 * g_height; mywidth = 0.24 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center'><span style='font-size:267%;color:#E9EB5D'><i>good<br> </i></span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.28 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center'><span style='font-size:267%;color:#E9EB5D'><i>candidates</i></span></div> </layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4><b>Candidate Genes: </b><span style="mso-spacerun: yes"> </span>The best we can do at this point is to make an educated guess about the candidacy status of all genes in the QTL support interval. For sake of argument, lets say that we are confident that the polymorphism is located between 130 and 150 Mb (20 Mb, equivalent to roughly 10 cM). There will typically be 12 to 15 genes per Mb, so we now would like to evaluate 240 to 300 positional candidates. We would like to highlight the biologically relevant subset of candidates. We could look through gene ontologies and expression levels to help us winnow the list. An alternate way avaiable using WebQTL is to generate a list of those genes in this 20 Mb interval that have transcripts that co-vary in expression with App expression.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>To do this, go back to the Trait Data and Editing window. Sort the correlations by position. Select Return = 500. Then scroll down the list to see positional candidates that share expression with App.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>There are several candidates that have high correlation with App even in this short 20 Mb interval. We can rank them by correlation, but they are all close.<span style="mso-spacerun: yes"> </span>There is one other imporant approach to ranking these candidates. Are they likely to contain polymorphisms? We can assess the likelihood that they contain polymorphisms by mapping each transcript to see if any have strong cis QTLs. The logic of this search is that a transcript that has a strong cis-QTL is likely to contain functional polymorphisms that effect its own expression. This make is more like that the transcript is a ÒcausativeÓ factor since it is likely to be polymorphic.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0054.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0054.htm new file mode 100755 index 00000000..1e0d7468 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0054.htm @@ -0,0 +1,125 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0054.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.01 * g_height; myleft = 0.03 * g_width; myheight = 0.13 * g_height; mywidth = 1.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.12 * g_height; mywidth = 1.02 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:16'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.02 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'><i>Only one of these candidates is a functional </i></span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.88 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'><i>polymorphism</i></span></span></layer></div> </layer></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0.02 * g_width; myheight = 0.84 * g_height; mywidth = 0.41 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.02 * g_width; +yy = 0.15 * g_height; +ht = 0.84 * g_height; +wd = 0.41 * g_width; +document.write( +'<img border=0 src="slide0022_image092.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.31 * g_height; myleft = 0.26 * g_width; myheight = 0.05 * g_height; mywidth = 0.27 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.26 * g_width; +yy = 0.31 * g_height; +ht = 0.05 * g_height; +wd = 0.27 * g_width; +document.write( +'<img border=0 src="slide0022_image093.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.28 * g_height; myleft = 0.54 * g_width; myheight = 0.21 * g_height; mywidth = 0.5 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.5 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-size:200%;color:#E9EB5D'><i>Hars2 = 0610006H08Rik<br> </i></span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.47 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:200%;color:#E9EB5D'><i>is a cis-QTL with a very </i></span></span></layer><script> + mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.42 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:200%;color:#E9EB5D'><i>high likelihood ratio </i></span></span></layer><script> + mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.42 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:200%;color:#E9EB5D'><i>statistic (LRS) score</i></span><span style='font-size:267%;color:#E9EB5D;mso-special-format: lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>When you do this you will find that only the transcript 0610006H08Rik has a strong cis QTL. See the slide above. The LRS peaks above 35<span style="mso-spacerun: yes"> </span>(LOD of greater than 7.5). It turns out that this transcript is really Hars2, also known as histydl tRNA synthase 2.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0055.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0055.htm new file mode 100755 index 00000000..36b2d736 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0055.htm @@ -0,0 +1,168 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0055.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.01 * g_height; myleft = 0.03 * g_width; myheight = 0.08 * g_height; mywidth = 1.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 1.02 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:16'><span style='font-size:233%;color:#E9EB5D'><i>Hars2 probe level analysis: 16 PMs mapped</i></span></div> </layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.13 * g_width; myheight = 0.84 * g_height; mywidth = 0.72 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.13 * g_width; +yy = 0.1 * g_height; +ht = 0.84 * g_height; +wd = 0.72 * g_width; +document.write( +'<img border=0 src="slide0023_image094.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.59 * g_height; myleft = 0.02 * g_width; myheight = 0.36 * g_height; mywidth = 0.41 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.02 * g_width; +yy = 0.59 * g_height; +ht = 0.36 * g_height; +wd = 0.41 * g_width; +document.write( +'<img border=0 src="slide0023_image095.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.6 * g_height; myleft = 0.36 * g_width; myheight = 0.19 * g_height; mywidth = 0.26 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.36 * g_width; +yy = 0.6 * g_height; +ht = 0.19 * g_height; +wd = 0.26 * g_width; +document.write( +'<img border=0 src="slide0023_image096.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.33 * g_height; myleft = 0.21 * g_width; myheight = 0.02 * g_height; mywidth = 0.64 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.21 * g_width; +yy = 0.33 * g_height; +ht = 0.02 * g_height; +wd = 0.64 * g_width; +document.write( +'<img border=0 src="slide0023_image097.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.21 * g_width; myheight = 0.02 * g_height; mywidth = 0.64 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.21 * g_width; +yy = 0.35 * g_height; +ht = 0.02 * g_height; +wd = 0.64 * g_width; +document.write( +'<img border=0 src="slide0023_image098.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.38 * g_height; myleft = 0.21 * g_width; myheight = 0.02 * g_height; mywidth = 0.64 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.21 * g_width; +yy = 0.38 * g_height; +ht = 0.02 * g_height; +wd = 0.64 * g_width; +document.write( +'<img border=0 src="slide0023_image099.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.19 * g_height; myleft = 0.2 * g_width; myheight = 0.21 * g_height; mywidth = 0.28 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.2 * g_width; +yy = 0.19 * g_height; +ht = 0.21 * g_height; +wd = 0.28 * g_width; +document.write( +'<img border=0 src="slide0023_image100.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.28 * g_height; myleft = 0.3 * g_width; myheight = 0.03 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-size:117%;color:#FF0F0F'><i>SNP</i></span></div> </layer><script> + mytop = 0.29 * g_height; myleft = 0.4 * g_width; myheight = 0.03 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:"100 50 0";mso-line-spacing:"100 50 0"'><span style='font-size:117%;color:#FF0F0F'>C in B6, T in D2 </span><span style='font-size:150%;color:black;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer><script> + mytop = 0.36 * g_height; myleft = 0.5 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-size:117%;color:#003399;mso-color-index: 4'><i>no SNPs</i></span></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>LetÕs look at Hars2 in more detail by mapping all of the perfect match probes (16 of them) that target this transcript.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Go back to the Trait Data and Editing window and select Chr 2 (rather than ALL as shown above) and also select PM Probes. Then click on Interval Mapping button.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>You will get the illustration above, but without the sequence data that we have added.<span style="mso-spacerun: yes"> </span>The 16 perfect match probes are arranged in sequence (red is 5 prime, blue is the 3 prime end). For example, the 5 prime-most primer 307387 has the sequence CACTG..... It also has a polymorphism at the 17 nucleotide of this 25 nt probe sequence.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>How do we know that the 5 prime probe is polymorphic? By looking up the sequence in the Celera Genomics databases which often contqains sequence data for C57BL/6J (B6 above) and for DBA/2J.<span style="mso-spacerun: yes"> </span>But two blue probes (14 and 15) do NOT contain SNPs but still have very large LRS scores. The other probes do not perform so wel. Highly variable probe performance is probably a result of the very different stacking energies of DNA-RNA duplexes.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0056.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0056.htm new file mode 100755 index 00000000..43ebf6d5 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0056.htm @@ -0,0 +1,129 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Tissue differences in probe performance"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0056.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.89 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0 * g_width; +yy = 0 * g_height; +ht = 0.89 * g_height; +wd = 0.08 * g_width; +document.write( +'<img border=0 src="slide0024_image101.gif" alt="Text Box: Tissue differences in probe performance" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.58 * g_height; myleft = 0.06 * g_width; myheight = 0.39 * g_height; mywidth = 0.62 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.06 * g_width; +yy = 0.58 * g_height; +ht = 0.39 * g_height; +wd = 0.62 * g_width; +document.write( +'<img border=0 src="slide0024_image102.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.17 * g_height; myleft = 0.74 * g_width; myheight = 0.07 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:300%; color:#E9EB5D'><i>Forebrain</i></span></div> </layer><script> + mytop = 0.79 * g_height; myleft = 0.74 * g_width; myheight = 0.07 * g_height; mywidth = 0.22 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:300%; color:#E9EB5D'><i>Stem cells</i></span></div> </layer><script> + mytop = 0.28 * g_height; myleft = 0.06 * g_width; myheight = 0.36 * g_height; mywidth = 0.62 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.06 * g_width; +yy = 0.28 * g_height; +ht = 0.36 * g_height; +wd = 0.62 * g_width; +document.write( +'<img border=0 src="slide0024_image103.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.06 * g_width; myheight = 0.36 * g_height; mywidth = 0.63 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.06 * g_width; +yy = 0 * g_height; +ht = 0.36 * g_height; +wd = 0.63 * g_width; +document.write( +'<img border=0 src="slide0024_image104.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.51 * g_height; myleft = 0.73 * g_width; myheight = 0.07 * g_height; mywidth = 0.25 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:300%; color:#E9EB5D'><i>Cerebellum</i></span></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The vertical text says it all: Even when using identical probes, mapping performance (and signal) depends on tissue type and mRNA complexity. This is another gene in the Hars2 interval. Forebrain and tem cell mRNAs were run on the same U74Av2 array, whereas the cerebellum mRNA was run on the 430A and 430B array set.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0057.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0057.htm new file mode 100755 index 00000000..9a7adf61 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0057.htm @@ -0,0 +1,122 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Is there known biology to link Hars2 with App? "> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0057.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = -0.03 * g_height; myleft = 0.02 * g_width; myheight = 0.18 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt:232; mso-text-indent-alt:0;mso-line-spacing:" 0 ";mso-margin-left-alt:232; mso-text-indent-alt:0'><span style='font-size:68%'><i>Is there known biology to link Hars2 with App? </i></span></div> </layer></div> </layer><script> + mytop = 0.82 * g_height; myleft = 0.04 * g_width; myheight = 0.18 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div></div> </layer><script> + mytop = 0.62 * g_height; myleft = 0.05 * g_width; myheight = 0.12 * g_height; mywidth = 0.29 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.29 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-size:150%;color:#E9EB5D;mso-color-index:3'><b>69 SNPs, 1 cSNP: <br> </b></span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.28 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-size:150%;color:#E9EB5D;mso-color-index:3'><b>6 exons in NCBI, <br> </b></span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.29 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-size:150%;color:#E9EB5D;mso-color-index:3'><b>2 exons in Celera</b></span></div> </layer></div> </layer><script> + mytop = 0.09 * g_height; myleft = 0.03 * g_width; myheight = 0.42 * g_height; mywidth = 0.6 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.03 * g_width; +yy = 0.09 * g_height; +ht = 0.42 * g_height; +wd = 0.6 * g_width; +document.write( +'<img border=0 src="slide0025_image105.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.28 * g_height; myleft = 0.4 * g_width; myheight = 0.69 * g_height; mywidth = 0.55 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.4 * g_width; +yy = 0.28 * g_height; +ht = 0.69 * g_height; +wd = 0.55 * g_width; +document.write( +'<img border=0 src="slide0025_image106.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.14 * g_height; myleft = 0.69 * g_width; myheight = 0.06 * g_height; mywidth = 0.23 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:250%; color:#E9EB5D'><i><span style="mso-spacerun: yes"> </span>Not obvious</i></span></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Hars2 is not a well characterized gene and their is no biology yet to support the hypothesis that Hars2 modulates gene expression, let alone App expression in specific. There are also serious database/assembly discrepancies between Celera and MGSCv3 regarding the genomic organization of this gene. But there appear to be approximately 69 SNPs in Hars2, one of which results in a substitution.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0058.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0058.htm new file mode 100755 index 00000000..9feed242 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0058.htm @@ -0,0 +1,135 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: WebQTL link to www.webqtl.org/search.html"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0058.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0.02 * g_width; myheight = 0.19 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.19 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt:232; mso-text-indent-alt:0;mso-line-spacing:" 0 ";mso-margin-left-alt:232; mso-text-indent-alt:0'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:68%'><i>WebQTL<span style="mso-spacerun: yes"> </span><br> </i></span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0.04 * g_width; myheight = 0.06 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:68%'><i>link to <br> </i></span></span></layer><script> + mytop = 0.11 * g_height; myleft = 0.04 * g_width; myheight = 0.08 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:86%'><i>www.webqtl.org/search.html</i></span><span style='font-size:68%;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </layer><script> + mytop = 0.36 * g_height; myleft = 0.02 * g_width; myheight = 0.45 * g_height; mywidth = 0.73 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.36 * g_height; mywidth = 0.71 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.67 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> + mytop = 0 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.62 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'><span style='mso-special-format:numbullet;color:#FBFDB8;position:absolute; left:-8.06%;font-family:Times;font-size:99%'>1.</span></span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Discovering shared expression </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.55 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>patterns<br> </span></span></layer></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.6 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> + mytop = 0 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.55 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'><span style='mso-special-format:numbullet;color:#FBFDB8;position:absolute; left:-9.09%;font-family:Times;font-size:99%'>2.</span></span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Discovering upstream </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.55 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>modulators (QTLs)<br> </span></span></layer></div> </layer><script> + mytop = 0.3 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.71 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> + mytop = 0 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.66 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'><span style='mso-special-format:numbullet;color:#FBFDB8;position:absolute; left:-7.61%;font-family:Times;font-size:99%'>3.</span></span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Discovering downstream targets</span></span></layer></div> </layer></div> </layer></div> </layer><script> + mytop = 0.82 * g_height; myleft = 0.04 * g_width; myheight = 0.18 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div></div> </layer><script> + mytop = 0.65 * g_height; myleft = 0.65 * g_width; myheight = 0.1 * g_height; mywidth = 0.26 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.65 * g_width; +yy = 0.65 * g_height; +ht = 0.1 * g_height; +wd = 0.26 * g_width; +document.write( +'<img border=0 src="slide0026_image107.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Part 3.<span style="mso-spacerun: yes"> </span>Many investigators would like to discover the set of downstream targets of a gene of interest.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>In a genetic and functional sense, that question can only be addressed effectively if there is genetic variation in the particular gene.<span style="mso-spacerun: yes"> </span>We know that Fos is an important transcription factor, but unless it is polymorphic between C57BL/6J and DBA/2J, then it cannot generate a genetic variance signal with which we can work. We can still study covariance of Fos and hundreds of other transcripts (an interesting exercise), but there are no genetic causes-and-effects.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0059.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0059.htm new file mode 100755 index 00000000..a479ea68 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0059.htm @@ -0,0 +1,128 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Requirement: The gene must be polymorphic to be genetically ÒupstreamÓ"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0059.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.02 * g_height; myleft = 0.02 * g_width; myheight = 0.18 * g_height; mywidth = 1.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 1.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-line-spacing:" 0 "'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 1.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:82%'><i>Requirement: The gene must be polymorphic to </i></span></span></layer><script> + mytop = 0.08 * g_height; myleft = 0.03 * g_width; myheight = 0.07 * g_height; mywidth = 0.85 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:82%'><i>be genetically ÒupstreamÓ</i></span><span style='font-size:82%;mso-special-format:lastCR; display:none'><br> </span></span></layer></div> </layer></div> </layer><script> + mytop = 0.21 * g_height; myleft = 0.02 * g_width; myheight = 0.15 * g_height; mywidth = 0.84 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.04 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-line-spacing:" 0 "'><span style='font-size:64%'><i>What are targets of the Hars2 polymorphisms?</i></span><span style='font-size:82%;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.33 * g_height; myleft = 0.01 * g_width; myheight = 0.32 * g_height; mywidth = 0.49 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.33 * g_height; +ht = 0.32 * g_height; +wd = 0.49 * g_width; +document.write( +'<img border=0 src="slide0027_image108.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.33 * g_height; myleft = 0.53 * g_width; myheight = 0.58 * g_height; mywidth = 0.44 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.53 * g_width; +yy = 0.33 * g_height; +ht = 0.58 * g_height; +wd = 0.44 * g_width; +document.write( +'<img border=0 src="slide0027_image109.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.69 * g_height; myleft = 0.07 * g_width; myheight = 0.21 * g_height; mywidth = 0.51 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.43 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>App and many other<br> </i></span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.51 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>correlated transcripts and </i></span></span></layer><script> + mytop = 0.14 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.43 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>other traits.</i></span></span></layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Genes must be polymorphic to generate downstream genetic effects (as opposed to downstream molecular effects). Hars2 meets this condition because we have already mapped a functional polymorphism in the gene. We can therefore posit that Hars2 is a QT gene. What transcripts are downstream? <i>App</i> is one obvious candidate, but there are many more.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The are several ways to look for downstream targets. The best and most obvious is to look up all transcripts that have high correlations with Hars2 itself. You should know how to do this. An alternative method is shown here for teaching purpose and to show you what to do if your gene of interest is not in our database. You need to know:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Times size=3>1.</font><font face=Verdana size=3> Where your gene is located. You need this information to find a surrogate marker; a marker that is located very close to your gene of interest.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. That your gene is polymorphic between C57BL/6J and DBA/2J.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>LetÕs look at the correlation of Hars2 with BXD genotypes as shown in the slide above to illustrate how to use markers as surrogate traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Go to the Trait Date and Editing window one more time. We want the data for Hars2 this time, not App. You should be able to show that Hars2 has a high<span style="mso-spacerun: yes"> </span>correlation with D2Mit423 as shown in the slide above.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>By clicking on the symbol D2Mit423 in the Correlation window, you will generate a new Trait Data window shown on the next slide.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0060.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0060.htm new file mode 100755 index 00000000..aa804b9a --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0060.htm @@ -0,0 +1,134 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Direct correlations between genotypes and traits"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0060.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = -0.01 * g_height; myleft = 0.02 * g_width; myheight = 0.11 * g_height; mywidth = 1.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-line-spacing:" 0 "'><span style='font-size:82%'><i>Direct correlations between genotypes and traits</i></span><span style='font-size:82%;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.22 * g_height; myleft = 0.03 * g_width; myheight = 0.42 * g_height; mywidth = 0.34 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.34 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>App and<br> </i></span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.34 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>correlated traits </i></span></span></layer><script> + mytop = 0.14 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.34 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>would be obvious </i></span></span></layer><script> + mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.34 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>candidates to </i></span></span></layer><script> + mytop = 0.28 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.34 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>correlate with </i></span></span></layer><script> + mytop = 0.35 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.34 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>D2Mit423</i></span></span></layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.33 * g_width; myheight = 0.87 * g_height; mywidth = 0.4 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.33 * g_width; +yy = 0.1 * g_height; +ht = 0.87 * g_height; +wd = 0.4 * g_width; +document.write( +'<img border=0 src="slide0028_image110.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.82 * g_height; myleft = 0.65 * g_width; myheight = 0.07 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.65 * g_width; +yy = 0.82 * g_height; +ht = 0.07 * g_height; +wd = 0.14 * g_width; +document.write( +'<img border=0 src="slide0028_image111.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.79 * g_height; myleft = 0.82 * g_width; myheight = 0.13 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>B = -1<br> </i></span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>D = 1</i></span></div> </layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>We can review the set of correlations between the marker D2Mit423 and all transcripts in forebrain.<span style="mso-spacerun: yes"> </span>This is in essence a backwards way of mapping QTLs. We are considering one marker and asking what traits correlate to the marker and how well.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0061.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0061.htm new file mode 100755 index 00000000..cce3b81c --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0061.htm @@ -0,0 +1,124 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: WhatÕs downstream of Chr 2 near Hars2?"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0061.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.11 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.95 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-line-spacing:" 0 "'><span style='font-size:82%'><i>WhatÕs downstream of Chr 2 near Hars2?</i></span><span style='font-size:82%;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.09 * g_height; myleft = 0.01 * g_width; myheight = 0.79 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.09 * g_height; +ht = 0.79 * g_height; +wd = 0.83 * g_width; +document.write( +'<img border=0 src="slide0029_image112.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.86 * g_height; myleft = 0.02 * g_width; myheight = 0.11 * g_height; mywidth = 1.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.03 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 1.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-line-spacing:" 0 "'><span style='font-size:64%'><i>Notice many Chr 2 hits: Linkage disequilibrium limits specificity</i></span><span style='font-size:64%;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.27 * g_height; myleft = 0.07 * g_width; myheight = 0.17 * g_height; mywidth = 0.22 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.07 * g_width; +yy = 0.27 * g_height; +ht = 0.17 * g_height; +wd = 0.22 * g_width; +document.write( +'<img border=0 src="slide0029_image113.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.24 * g_height; myleft = 0.27 * g_width; myheight = 0.04 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-size:150%;color:#FF0F0F'><b>Click here</b></span></div> </layer><script> + mytop = 0.39 * g_height; myleft = 0.48 * g_width; myheight = 0.05 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.48 * g_width; +yy = 0.39 * g_height; +ht = 0.05 * g_height; +wd = 0.12 * g_width; +document.write( +'<img border=0 src="slide0029_image114.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The marker D2Mit423 correlates moderately well with a number of Chr 2 transcripts. This is due to linkage disequilibrium. These correlations are not due to a molecular interactions other than being close together on a chromosome.<span style="mso-spacerun: yes"> </span>But we have circled one transcript, actinin alpha 2, that has a moderately good correlation (0.59) with D2Mit423. If we map this gene we expect to find a suggestive QTL that peaks near D2Mit423</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0062.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0062.htm new file mode 100755 index 00000000..c8c24f70 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0062.htm @@ -0,0 +1,96 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: WhatÕs downstream of Chr 2 near Hars2?"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0062.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.11 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.95 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-line-spacing:" 0 "'><span style='font-size:82%'><i>WhatÕs downstream of Chr 2 near Hars2?</i></span><span style='font-size:82%;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.12 * g_height; myleft = 0.07 * g_width; myheight = 0.75 * g_height; mywidth = 0.61 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.07 * g_width; +yy = 0.12 * g_height; +ht = 0.75 * g_height; +wd = 0.61 * g_width; +document.write( +'<img border=0 src="slide0030_image115.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.9 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 1.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:233%; color:#E9EB5D'><i>modest support that Actn2 is modulated by the Hars2 region</i></span></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>There is some support for the hypothesis that Actn2 is downstream of a polymorphism in the Hars2 region. But again, due to the 10 to 20 Mb precision of the mapping data, this relation could be generated by a large number of other polymorphisms close to Hars2. In the absence of a biological connection between Actn2 and Hars2 we have a weak hypothesis. If there were a plausible functional connection between the two genes, then this hypothesis could be quickly upgraded.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0063.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0063.htm new file mode 100755 index 00000000..53358da8 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0063.htm @@ -0,0 +1,139 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Does Hars2 correlate with Actn2 strongly?"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0063.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = -0.01 * g_height; myleft = 0.02 * g_width; myheight = 0.09 * g_height; mywidth = 0.95 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 0.92 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-line-spacing:" 0 "'><span style='font-size:73%'><i>Does Hars2 correlate with Actn2 strongly?</i></span><span style='font-size:82%;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.02 * g_width; myheight = 0.28 * g_height; mywidth = 0.47 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.02 * g_width; +yy = 0.07 * g_height; +ht = 0.28 * g_height; +wd = 0.47 * g_width; +document.write( +'<img border=0 src="slide0031_image116.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.33 * g_height; myleft = 0.3 * g_width; myheight = 0.66 * g_height; mywidth = 0.67 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.3 * g_width; +yy = 0.33 * g_height; +ht = 0.66 * g_height; +wd = 0.67 * g_width; +document.write( +'<img border=0 src="slide0031_image117.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.17 * g_height; myleft = 0.33 * g_width; myheight = 0.15 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.33 * g_width; +yy = 0.17 * g_height; +ht = 0.15 * g_height; +wd = 0.15 * g_width; +document.write( +'<img border=0 src="slide0031_image118.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.41 * g_height; myleft = 0.02 * g_width; myheight = 0.42 * g_height; mywidth = 0.28 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.26 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>Plenty of high </i></span></span></layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.25 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>correlations, </i></span></span></layer><script> + mytop = 0.14 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.25 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>including 2 </i></span></span></layer><script> + mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.28 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>actins, but not </i></span></span></layer><script> + mytop = 0.28 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.25 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>to Actn2 </i></span></span></layer><script> + mytop = 0.35 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.25 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>specifically.</i></span></span></layer></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0.52 * g_width; myheight = 0.06 * g_height; mywidth = 0.25 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>Sort by gene</i></span></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>We can test the Hars2 to Actn2 connection directly. This process weakens the putative association. We are ready to move on and examine other candidates in the Hars2 region near D2Mit423.<span style="mso-spacerun: yes"> </span>Or in your case, please start from the beginning using other genes and transcripts and tissues that interest you more than this App-Hsp84-Hars2 example.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>This concludes the first demonstation of how to use some of the WebQTL features. Please explore. Please also send feedback for improvements or additions to rwilliam@nb.utmem.edu</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0064.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0064.htm new file mode 100755 index 00000000..f75dd8f4 --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0064.htm @@ -0,0 +1,100 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jun-19-03: Contact for comments and improvements:"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0064.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; 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+</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.02 * g_height; myleft = 0.02 * g_width; myheight = 0.1 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 0.92 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-line-spacing:" 0 "'><span style='font-size:73%'><i>Contact for comments and improvements:</i></span><span style='font-size:82%;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.12 * g_height; myleft = 0.06 * g_width; myheight = 0.32 * g_height; mywidth = 0.9 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.32 * g_height; mywidth = 0.87 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 ";mso-line-spacing:" 0 "'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.87 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:82%'>rwilliam@ nb.utmem.edu<br> </span></span></layer><script> + mytop = 0.08 * g_height; myleft = 0.04 * g_width; myheight = 0.07 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:82%'>kenneth.manly@roswellpark.org<br> </span></span></layer><script> + mytop = 0.16 * g_height; myleft = 0.04 * g_width; myheight = 0.07 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:82%'>lulu@ nb.utmem.edu<br> </span></span></layer><script> + mytop = 0.24 * g_height; myleft = 0.04 * g_width; myheight = 0.07 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:82%'>echesler@ nb.utmem.edu</span></span></layer></div> </layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>END</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0065.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0065.htm new file mode 100755 index 00000000..df6b13dd --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0065.htm @@ -0,0 +1,34 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); 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+} +</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript> + if ( parent.base.msie < 0 ) { + document.captureEvents(Event.MOUSEDOWN); + document.captureEvents(Event.KEYPRESS); + document.onkeypress = _KPH; + document.onmousedown = _KPH; + } + +function restore() { + if ( parent.base.msie < 0 ) + self.location.reload(); +} +</script> +<script language=JavaScript> +function flatLoad() { +if ( !parent.IsFullScrMode() ) + parent.base.highlite(); +DoOnLoad(); + + + if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed ) + parent.NavPopup.focus(); + else + self.focus(); + parent.base.SldUpdated( "slide0068.htm" ); + } + </script><script language=JavaScript><!-- +function DoOnLoad() { + }//--> +</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0004.gif border=0 usemap="#Slide0004.gif_map"></center> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0069.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0069.htm new file mode 100755 index 00000000..4b91f9fb --- /dev/null +++ b/web/tutorial/ppt/WebQTLDemo_files/slide0069.htm @@ -0,0 +1,34 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 10"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href=WebQTLDemo.ppt> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); 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new file mode 100755 index 00000000..b696e328 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/master02.htm @@ -0,0 +1,11 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Robots content=NoIndex> <link rel=Stylesheet href="master03_stylesheet.css"> <script language=JavaScript src=script.js></script> +<script> +<!-- + parent.location.href=document.all.item("Main-File").href +//--> +</script> + </head> <body> <div class=O style='text-align:right;position:absolute;top:.53%;left:58.01%; width:40.79%;height:2.12%'><span style='color:black'><b>Memphis 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b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_collapsed.htm new file mode 100755 index 00000000..9e7d7d90 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_collapsed.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Robots content=NoIndex> <style> <!--a {text-decoration: none;}--> </style> </head> <body bgcolor=black text=white link=white vlink=white alink=white onload=" parent.base.highlite();" onresize="self.location.reload();"> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID1 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p1" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('1')" id=AREF>The GeneNetwork and WebQTL : PART 2<span style="mso-spacerun: yes"> </span><br> link to www.genenetwork.org</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID2 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p2" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('2')" id=AREF>Slide 2</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID3 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p3" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('3')" id=AREF>Slide 3</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID4 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p4" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('4')" id=AREF><font face=Verdana>Discovering upstream modulatory loci</font></a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID5 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p5" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('5')" id=AREF>WebQTL searches for upstream controllers</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID6 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p6" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('6')" id=AREF>Genetic versus Physical maps for App expression</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID7 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p7" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('7')" id=AREF>Physical map for distal chromosome 7</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID8 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p8" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('8')" id=AREF>Evaluating candidate genes</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID9 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p9" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('9')" id=AREF>Physical maps are zoomable</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID10 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p10" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('10')" id=AREF>Evaluating Ctbp2 as a candidate QTL for App</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID11 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p11" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('11')" id=AREF>Evaluating Ctbp2 using other resources</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID12 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p12" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('12')" id=AREF>"Summary of Part 2"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID13 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p13" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('13')" id=AREF>Test Questions</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID14 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p14" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('14')" id=AREF>Contact for comments and improvements:</a></b></font></td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_expand.gif b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_expand.gif new file mode 100755 index 00000000..c8c72b13 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_expand.gif Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_expanded.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_expanded.htm new file mode 100755 index 00000000..c33cf334 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_expanded.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Robots content=NoIndex> <style> <!--a {text-decoration: none;}--> </style> </head> <body bgcolor=black text=white link=white vlink=white alink=white onload=" parent.base.highlite();" onresize="self.location.reload();"> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID1 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p1" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('1')" id=AREF>The GeneNetwork and WebQTL : PART 2<span style="mso-spacerun: yes"> </span><br> link to www.genenetwork.org</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Part 1. How to study expression variation and genetic correlation (slides 2–17)</font></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Part 2. Discovering upstream modulators (slides 18–29)</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID2 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p2" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('2')" id=AREF>Slide 2</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID3 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p3" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('3')" id=AREF>Slide 3</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID4 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p4" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('4')" id=AREF><font face=Verdana>Discovering upstream modulatory loci</font></a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID5 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p5" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('5')" id=AREF>WebQTL searches for upstream controllers</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID6 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p6" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('6')" id=AREF>Genetic versus Physical maps for App expression</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID7 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p7" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('7')" id=AREF>Physical map for distal chromosome 7</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID8 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p8" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('8')" id=AREF>Evaluating candidate genes</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID9 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p9" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('9')" id=AREF>Physical maps are zoomable</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID10 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p10" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('10')" id=AREF>Evaluating Ctbp2 as a candidate QTL for App</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID11 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p11" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('11')" id=AREF>Evaluating Ctbp2 using other resources</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID12 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p12" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('12')" id=AREF>"Summary of Part 2"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Summary of Part 2</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID13 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p13" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('13')" id=AREF>Test Questions</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID14 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p14" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('14')" id=AREF>Contact for comments and improvements:</a></b></font></td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_navigation_bar.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_navigation_bar.htm new file mode 100755 index 00000000..85b11c52 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_navigation_bar.htm @@ -0,0 +1,37 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); 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+function LoadSld( slideId ) +{ + if( !g_supportsPPTHTML ) return + if( slideId ) + parent.base.SldUpdated(slideId) + g_origSz=parseInt(SlideObj.style.fontSize) + g_origH=SlideObj.style.posHeight + g_origW=SlideObj.style.posWidth + g_scaleHyperlinks=(document.all.tags("AREA").length>0) + if ( IsWin("PPTSld") && !parent.IsFullScrMode() ) + parent.base.highlite(); + if( g_scaleHyperlinks ) + InitHLinkArray() + if( g_scaleInFrame||(IsWin("PPTSld") && parent.IsFullScrMode() ) ) + document.body.scroll="no" + _RSW() + if( IsWin("PPTSld") && (parent.IsFullScrMode() || CtxAlwaysOn ) ) { + document.oncontextmenu=parent._CM; + self.focus(); + + } +} +function MakeSldVis( fTrans ) +{ + fTrans=fTrans && g_showAnimation + if( fTrans ) + { + if( g_bgSound ) { + idx=g_bgSound.indexOf(","); + pptSound.src=g_bgSound.substr( 0, idx ); + pptSound.loop= -(parseInt(g_bgSound.substr(idx+1))); + } + SlideObj.filters.revealtrans.Apply() + } + SlideObj.style.visibility="visible" + if( fTrans ) + SlideObj.filters.revealtrans.Play() +} +function MakeNotesVis() +{ + if( !IsNts() ) return false + SlideObj.style.display="none" + nObj = document.all.item("NotesObj") + parent.SetHasNts(0) + if( nObj ) { + nObj.style.display="" + parent.SetHasNts(1) + } + return 1 +} +function Redirect( frmId,sId ) +{ + var str=document.location.hash,idx=str.indexOf('#') + if(idx>=0) str=str.substr(1); + if( window.name != frmId && ( sId != str) ) { + obj = document.all.item("Main-File") + window.location.href=obj.href+"#"+sId + return 1 + } + return 0 +} +function HideMenu() { if( frames["PPTSld"] && PPTSld.document.all.item("ctxtmenu") && PPTSld.ctxtmenu.style.display!="none" ) { PPTSld.ctxtmenu.style.display='none'; return true } return false } +function IsWin( name ) { return window.name == name } +function IsNts() { return IsWin("PPTNts") } +function IsSldOrNts() { return( IsWin("PPTSld")||IsWin("PPTNts") ) } +function SupportsPPTAnimation() { return( navigator.platform == "Win32" && navigator.appVersion.indexOf("Windows")>0 ) } +function SupportsPPTHTML() +{ + var appVer=navigator.appVersion, msie=appVer.indexOf( "MSIE " ), inex = appVer.indexOf( "Internet Explorer " ), ver=0 + if( msie >= 0 ) + ver=parseFloat( appVer.substring( msie+5, appVer.indexOf(";",msie) ) ) + else if( inex >= 0 ) + ver=parseFloat( appVer.substring( inex+18, appVer.indexOf(";",inex) ) ) + else + ver=parseInt(appVer) + + return( ver >= 4 ) +} +var MHTMLPrefix = CalculateMHTMLPrefix(); +function CalculateMHTMLPrefix() +{ + if ( document.location.protocol == 'mhtml:') { + href=new String(document.location.href) + Start=href.indexOf('!')+1 + End=href.lastIndexOf('/')+1 + if (End < Start) + return href.substring(0, Start) + else + return href.substring(0, End) + } + return ''; +} + +function LoadNavSld(slideId) { +playList(); +parent.createCM(); + if( !g_supportsPPTHTML ) return + if( IsWin("PPTSld") && slideId ) + parent.base.SldUpdated(slideId) + self.focus(); + +} +var hasNarration = false; +function _RSW() +{ + if( !g_supportsPPTHTML || IsNts() || + ( !g_scaleInFrame && (( window.name != "PPTSld" ) ) ) ) + return + + cltWidth=document.body.clientWidth + cltHeight=document.body.clientHeight + factor=(1.0*cltWidth)/g_origW + if( cltHeight < g_origH*factor ) + factor=(1.0*cltHeight)/g_origH + + newSize = g_origSz * factor + if( newSize < 1 ) newSize=1 + + s=SlideObj.style + s.fontSize=newSize+"px" + s.posWidth=g_origW*factor + s.posHeight=g_origH*factor + s.posLeft=(cltWidth-s.posWidth)/2 + s.posTop=(cltHeight-s.posHeight)/2 + + if ( hasNarration ) { + obj = document.all.NSPlay.style; + mySld = document.all.SlideObj.style; + obj.position = 'absolute'; + obj.posTop = mySld.posTop + mySld.posHeight - 20; + obj.posLeft = mySld.posLeft + mySld.posWidth - 20; + } + if( g_scaleHyperlinks ) + ScaleHyperlinks( factor ); +} +function IsMac() { + return (window.navigator.platform.indexOf("Mac") >= 0 ); +} + +function HitOK( evt ) { + //Nav Only function + return (evt.which == 1 || (IsMac() && evt.which == 3) ); +} +function _KPH(event) +{ + + if ( parent.base.msie < 0 ) { + + if ( ( (event.target.name && event.target.name == "hasMap" ) || (event.target.href && event.target.href != "") ) && parent.g_docTable[0].type != "jpeg" && HitOK( event ) ) { + return; /* to make hyperlinks in fullscreen mode traversable */ + } + if( IsContextMenu() ) + return parent.KPH(event); + if ( parent.IsFullScrMode() && event.which == 27 ) + parent.base.CloseFullScreen(); + else if ( parent.base.IsFullScrMode() && ( (!IsMac() && event.which == 3) || ( IsMac() && (event.modifiers & Event.CONTROL_MASK) && event.which == 1 ) ) ) + return parent.KPH(event); + else if( (event.which == 32) || (event.which == 13) || HitOK( event ) ) { + if( window.name == "PPTSld" ) + parent.PPTSld.DocumentOnClick(); + else + parent.M_GoNextSld(); + } + else if ( parent.IsFullScrMode() && ((event.which == 78) || (event.which == 110) || (event.which == 29) || (event.which == 31) || (event.which == 12)) ) + parent.M_GoNextSld(); + else if ( parent.IsFullScrMode() && ( (event.which == 80) || (event.which == 112) || (event.which == 30) || (event.which == 28) || (event.which == 11) || (event.which == 8)) ) + parent.M_GoPrevSld(); + + return; + } + + if( IsNts() ) return; + + if(parent.IsFullScrMode() && event.keyCode == 27 && !parent.HideMenu() ) + parent.base.CloseFullScreen(); + else if( (event.keyCode == 32) || (event.keyCode == 13) ) + { + if( window.name == "PPTSld" ) + parent.PPTSld.DocumentOnClick(); + else + parent.M_GoNextSld(); + } + else if ( parent.IsFullScrMode() && ((event.keyCode == 78) || (event.keyCode == 110)) ) + parent.M_GoNextSld(); + else if ( parent.IsFullScrMode() && ((event.keyCode == 80) || (event.keyCode == 112)) ) + parent.M_GoPrevSld(); +} + +function DocumentOnClick(event) +{ + if ( g_doAdvOnClick && !parent.IsFullScrMode() ) { + parent.base.TP_GoToNextSld(); + return; + } + + if ( parent.base.msie < 0 ) + { + if( ( g_allowAdvOnClick && parent.IsFullScrMode() ) || g_doAdvOnClick || + (event && ( (event.which == 32) || (event.which == 13) ) ) ) + parent.M_GoNextSld(); + return; + } + if( IsNts() || (parent.IsFullScrMode() && parent.HideMenu() ) ) return; + if( ( g_allowAdvOnClick && parent.IsFullScrMode() ) || g_doAdvOnClick || + (event && ( (event.keyCode==32) || (event.keyCode == 13) ) ) ) + parent.M_GoNextSld(); +} + + +var g_supportsPPTHTML = SupportsPPTHTML(), g_scaleInFrame = true, gId="", g_bgSound="", + g_scaleHyperlinks = false, g_allowAdvOnClick = true, g_showInBrowser = false, g_doAdvOnClick = false; + + var g_showAnimation = 0; +var g_hasTrans = false, g_autoTrans = false, g_transSecs = 0; +var g_animManager = null; + +var ENDSHOW_MESG="End of slide show, click to exit.", SCREEN_MODE="Frames", gIsEndShow=0, NUM_VIS_SLDS=14, SCRIPT_HREF="script.js", FULLSCR_HREF="fullscreen.htm"; +var gCurSld = gPrevSld = 1, g_offset = 0, gNtsOpen = gHasNts = gOtlTxtExp = gNarrationPaused = false, gOtlOpen = true +window.gPPTHTML=SupportsPPTHTML() +var g_hideNav = 0; +function UpdNtsPane(){ PPTNts.location.replace( MHTMLPrefix+GetHrefObj( gCurSld ).mNtsHref ) } +function UpdNavPane( sldIndex ){ if(gNavLoaded) PPTNav.UpdNav() } +function UpdOtNavPane(){ if(gOtlNavLoaded) PPTOtlNav.UpdOtlNav() } +function UpdOtlPane(){ if(gOtlLoaded) PPTOtl.UpdOtl() } +function SetHasNts( fVal ) +{ + if( gHasNts != fVal ) { + gHasNts=fVal + UpdNavPane() + } +} + +function ToggleVNarration() +{ + if ( base.msie < 0 ) { + PPTSld.ToggleSound( false, PPTSld.document.NSPlay ); + return; + } + + rObj=PPTSld.document.all("NSPlay") + if( rObj ) { + if( gNarrationPaused ) + rObj.Play() + else + rObj.Pause() + + gNarrationPaused=!gNarrationPaused + } +} + +function PrevSldViewed(){ GoToSld( GetHrefObj(gPrevSld).mSldHref ) } +function HasPrevSld() { return ( gIsEndShow || ( g_currentSlide != 1 && GetHrefObj( g_currentSlide-1 ).mVis == 1 )||( GetCurrentSlideNum() > 1 ) ) } +function HasNextSld() { return (GetCurrentSlideNum() != GetNumSlides()) } +function StartEndShow() +{ +// g_hideNav = 1; +// PPTNav.location.reload(); + if( PPTSld.event ) PPTSld.event.cancelBubble=true + + doc=PPTSld.document + doc.open() + doc.writeln('<html><head><script > /*defer>*/ g_ctxmenu = 0; ' + + 'if( parent.base.msie < 0 ) { document.captureEvents(Event.KEYPRESS); document.captureEvents(Event.MOUSEDOWN); document.onkeypress = _KPH; document.onmousedown = _KPH; } ' + + 'function DocumentOnClick(event) { return _KPH(event); } function IsContextMenu() { return (g_ctxmenu ==1); } ' + + 'function _KPH(event)' + + '{ ' + + 'if ( parent.base.msie < 0 && (parent.IsFullScrMode() ) && event ) { if ( (!parent.IsMac() && event.which == 3) || ( parent.IsMac() && (event.modifiers & Event.CONTROL_MASK) && event.which == 1 ) ) { return parent.KPH(event); } ' + + ' else if (event.which == 27 || event.which == 32 || event.which == 13 || parent.HitOK( event ) || (event.which == 78) || (event.which == 110) || (event.which == 29) || (event.which == 31) || (event.which == 12) ) { if ( IsContextMenu() ) { return parent.KPH(event); } parent.base.CloseFullScreen(); return; } ' + + ' else if ( (event.which == 80) || (event.which == 112) || (event.which == 30) || (event.which == 28) || (event.which == 11) || (event.which == 8) ) { parent.M_GoPrevSld(); } } ' + + 'if( parent.HideMenu() ) return; if( (parent.IsFullScrMode() ) && event) { if ( (event.keyCode==27 || event.keyCode == 13 || event.keyCode==32 || event.type=="click" ) || (event.keyCode == 78) || (event.keyCode == 110) ) { parent.base.CloseFullScreen(); }' + + ' else if ( (event.keyCode == 80) || (event.keyCode == 112) ) { parent.M_GoPrevSld(); } } } function Unload() { parent.gIsEndShow=0; } function SetupEndShow() { if ( !parent.IsFullScrMode() ) { return; } else { parent.PPTNav.location.reload(); } parent.gIsEndShow=1; if ( parent.g_docTable[0].type != "jpeg" ) { if ( parent.base.msie < 0 ) {parent.createCM(); } document.oncontextmenu=parent._CM; } }</script></head><body scroll=\"no\" onclick=\"DocumentOnClick(event)\" onkeypress=\"_KPH(event)\" bgcolor=\"black\" onload=\"SetupEndShow()\" onunload=\"Unload()\"><center><p><font face=Tahoma color=white size=2><br><b>' + ENDSHOW_MESG + '</b></font></p></center></body></html>') + doc.close() +} +function SetSldVisited(){ gDocTable[gCurSld-1].mVisited=true } +function IsSldVisited(){ return gDocTable[gCurSld-1].mVisited } +function hrefList( sldHref, visible, sldIdx ) +{ + this.mSldHref= this.mNtsHref = sldHref + this.mSldIdx = sldIdx + this.mOrigVis= this.mVis = visible + this.mVisited= false +} +var gDocTable = new Array( + new hrefList("slide0001.htm", 1, 1), + new hrefList("slide0002.htm", 1, 2), + new hrefList("slide0003.htm", 1, 3), + new hrefList("slide0004.htm", 1, 4), + new hrefList("slide0005.htm", 1, 5), + new hrefList("slide0006.htm", 1, 6), + new hrefList("slide0007.htm", 1, 7), + new hrefList("slide0008.htm", 1, 8), + new hrefList("slide0009.htm", 1, 9), + new hrefList("slide0010.htm", 1, 10), + new hrefList("slide0011.htm", 1, 11), + new hrefList("slide0012.htm", 1, 12), + new hrefList("slide0013.htm", 1, 13), + new hrefList("slide0014.htm", 1, 14) +); + +function ImgBtn( oId,bId,w,action ) +{ + var t=this + t.Perform = _IBP + t.SetActive = _IBSetA + t.SetInactive= _IBSetI + t.SetPressed = _IBSetP + t.SetDisabled= _IBSetD + t.Enabled = _IBSetE + t.ChangeIcon = null + t.UserAction = action + t.ChgState = _IBUI + t.mObjId = oId + t.mBorderId= bId + t.mWidth = w + t.mIsOn = t.mCurState = 0 +} +function _IBSetA() +{ + if( this.mIsOn ) { + obj=this.ChgState( gHiliteClr,gShadowClr,2 ) + obj.style.posTop=0 + } +} +function _IBSetI() +{ + if( this.mIsOn ) { + obj=this.ChgState( gFaceClr,gFaceClr,1 ) + obj.style.posTop=0 + } +} +function _IBSetP() +{ + if( this.mIsOn ) { + obj=this.ChgState( gShadowClr,gHiliteClr,2 ) + obj.style.posLeft+=1; obj.style.posTop+=1 + } +} +function _IBSetD() +{ + obj=this.ChgState( gFaceClr,gFaceClr,0 ) + obj.style.posTop=0 +} +function _IBSetE( state ) +{ + var t=this + GetObj( t.mBorderId ).style.visibility="visible" + if( state != t.mIsOn ) { + t.mIsOn=state + if( state ) + t.SetInactive() + else + t.SetDisabled() + } +} +function _IBP() +{ + var t=this + if( t.mIsOn ) { + if( t.UserAction != null ) + t.UserAction() + if( t.ChangeIcon ) { + obj=GetObj(t.mObjId) + if( t.ChangeIcon() ) + obj.style.posLeft=obj.style.posLeft+(t.mCurState-4)*t.mWidth + else + obj.style.posLeft=obj.style.posLeft+(t.mCurState-0)*t.mWidth + } + t.SetActive() + } +} +function _IBUI( clr1,clr2,nextState ) +{ + var t=this + SetBorder( GetObj( t.mBorderId ),clr1,clr2 ) + obj=GetObj( t.mObjId ) + obj.style.posLeft=obj.style.posLeft+(t.mCurState-nextState)*t.mWidth-obj.style.posTop + t.mCurState=nextState + return obj +} +function TxtBtn( oId,oeId,action,chkState ) +{ + var t=this + t.Perform = _TBP + t.SetActive = _TBSetA + t.SetInactive= _TBSetI + t.SetPressed = _TBSetP + t.SetDisabled= _TBSetD + t.SetEnabled = _TBSetE + t.GetState = chkState + t.UserAction = action + t.ChgState = _TBUI + t.mObjId = oId + t.m_elementsId= oeId + t.mIsOn = 1 +} +function _TBSetA() +{ + var t=this + if( t.mIsOn && !t.GetState() ) + t.ChgState( gHiliteClr,gShadowClr,0,0 ) +} +function _TBSetI() +{ + var t=this + if( t.mIsOn && !t.GetState() ) + t.ChgState( gFaceClr,gFaceClr,0,0 ) +} +function _TBSetP() +{ + if( this.mIsOn ) + this.ChgState( gShadowClr,gHiliteClr,1,1 ) +} +function _TBSetD() +{ + this.ChgState( gFaceClr,gFaceClr,0,0 ) + this.mIsOn = 0 +} +function _TBSetE() +{ + var t=this + if( !t.GetState() ) + t.ChgState( gFaceClr,gFaceClr,0,0 ) + else + t.ChgState( gShadowClr,gHiliteClr,1,1 ) + t.mIsOn = 1 +} +function _TBP() +{ + var t=this + if( t.mIsOn ) { + if( t.UserAction != null ) + t.UserAction() + if( t.GetState() ) + t.SetPressed() + else + t.SetActive() + } +} +function _TBUI( clr1,clr2,lOffset,tOffset ) +{ + SetBorder( GetObj( this.mObjId ),clr1,clr2 ) + Offset( GetObj( this.m_elementsId ),lOffset,tOffset ) +} +function GetObj( objId ){ return document.all.item( objId ) } +function Offset( obj, top, left ){ obj.style.top=top; obj.style.left=left } +function SetBorder( obj, upperLeft, lowerRight ) +{ + s=obj.style; + s.borderStyle = "solid" + s.borderWidth = 1 + s.borderLeftColor = s.borderTopColor = upperLeft + s.borderBottomColor= s.borderRightColor = lowerRight +} +function GetBtnObj(){ return gBtnArr[window.event.srcElement.id] } +function BtnOnOver(){ b=GetBtnObj(); if( b != null ) b.SetActive() } +function BtnOnDown(){ b=GetBtnObj(); if( b != null ) b.SetPressed() } +function BtnOnOut(){ b=GetBtnObj(); if( b != null ) b.SetInactive() } +function BtnOnUp() +{ + b=GetBtnObj() + if( b != null ) + b.Perform() + else + Upd() +} +function GetNtsState(){ return parent.gNtsOpen } +function GetOtlState(){ return parent.gOtlOpen } +function GetOtlTxtState(){ return parent.gOtlTxtExp } +function NtsBtnSetFlag( fVal ) +{ + s=document.all.item( this.m_flagId ).style + s.display="none" + if( fVal ) + s.display="" + else + s.display="none" +} + +var gHiliteClr="THREEDHIGHLIGHT",gShadowClr="THREEDSHADOW",gFaceClr="THREEDFACE" +var gBtnArr = new Array() +gBtnArr["nb_otl"] = new TxtBtn( "nb_otl","nb_otlElem",parent.ToggleOtlPane,GetOtlState ) +gBtnArr["nb_nts"] = new TxtBtn( "nb_nts","nb_ntsElem",parent.ToggleNtsPane,GetNtsState ) +gBtnArr["nb_prev"]= new ImgBtn( "nb_prev","nb_prevBorder",30,parent.GoToPrevSld ) +gBtnArr["nb_next"]= new ImgBtn( "nb_next","nb_nextBorder",30,parent.GoToNextSld ) +gBtnArr["nb_sldshw"]= new ImgBtn( "nb_sldshw","nb_sldshwBorder",18,parent.FullScreen ) +gBtnArr["nb_voice"] = new ImgBtn( "nb_voice","nb_voiceBorder",18,parent.ToggleVNarration ) +gBtnArr["nb_otlTxt"]= new ImgBtn( "nb_otlTxt","nb_otlTxtBorder",23,parent.ToggleOtlText ) +gBtnArr["nb_nts"].m_flagId= "notes_flag" +gBtnArr["nb_nts"].SetFlag = NtsBtnSetFlag +gBtnArr["nb_otlTxt"].ChangeIcon= GetOtlTxtState +var sNext="Next",sPrev="Previous",sEnd="End Show",sFont="Arial", alwaysOn = false +function ShowMenu() +{ + BuildMenu(); + var doc=PPTSld.document.body,x=PPTSld.event.clientX+doc.scrollLeft,y=PPTSld.event.clientY+doc.scrollTop + + m = PPTSld.document.all.item("ctxtmenu") + m.style.pixelLeft=x + if( (x+m.scrollWidth > doc.clientWidth)&&(x-m.scrollWidth > 0) ) + m.style.pixelLeft=x-m.scrollWidth + + m.style.pixelTop=y + if( (y+m.scrollHeight > doc.clientHeight)&&(y-m.scrollHeight > 0) ) + m.style.pixelTop=y-m.scrollHeight + + m.style.display="" +} +function _CM() +{ + if( !parent.IsFullScrMode() && !alwaysOn) return; + + if(!PPTSld.event.ctrlKey) { + ShowMenu() + return false + } else + HideMenu() +} + +function processNavKPH(event) { + if ( PPTSld && (event.keyCode != 13 || !event.srcElement.href || event.srcElement.href == "" ) ) + return PPTSld._KPH(event); +} +function processNavClick() { + HideMenu(); + return true; +} +function BuildMenu() +{ + if( PPTSld.document.all.item("ctxtmenu") ) return + + var mObj=CreateItem( PPTSld.document.body ) +mObj.id="ctxtmenu" + var s=mObj.style + s.position="absolute" + s.cursor="default" + s.width="100px" + SetCMBorder(mObj,"menu","black") + + var iObj=CreateItem( mObj ) + SetCMBorder( iObj, "threedhighlight","threedshadow" ) + iObj.style.padding=2 + if ( self.IsFullScrMode() ) { + CreateMenuItem( iObj,sNext,M_GoNextSld,M_True ) + CreateMenuItem( iObj,sPrev,M_GoPrevSld,M_HasPrevSld ) + } + else { + CreateMenuItem( iObj,sNext, base.TP_GoToNextSld, base.HasNextSld ) + CreateMenuItem( iObj,sPrev,base.GoToPrevSld, base.HasPrevSld ) + } + var sObj=CreateItem( iObj ) + SetCMBorder(sObj,"menu","menu") + var s=sObj.style + s.borderTopColor="threedshadow" + s.borderBottomColor="threedhighlight" + s.height=1 + s.fontSize="0px" + if ( self.IsFullScrMode() ) + CreateMenuItem( iObj,sEnd,M_End,M_True ) + else + CreateMenuItem( iObj,sEnd,M_End,M_False ) +} +function Highlight() { ChangeClr("activecaption","threedhighlight") } +function Deselect() { ChangeClr("threedface","menutext") } +function Perform() +{ + e=PPTSld.event.srcElement + if( e.type=="menuitem" && e.IsActive() ) + e.Action() + else + PPTSld.event.cancelBubble=true +} +function ChangeClr( bg,clr ) +{ + e=PPTSld.event.srcElement + if( e.type=="menuitem" && e.IsActive() ) { + e.style.backgroundColor=bg + e.style.color=clr + } +} + +function M_HasPrevSld() { return( base.HasPrevSld() ) } +function M_GoNextSld() { + base.SetFSMode(1); + if( gIsEndShow ) + M_End(); + else { + if ( base.HasNextSld() ) + base.GoToNextSld(); + else if ( base.EndSlideShow ) { + StartEndShow(); + gIsEndShow = 1; + + PPTNav.location.reload(); + } + else + base.CloseFullScreen(); + } +} +function M_GoPrevSld() { + base.SetFSMode(1); + g_hideNav = 0; + if( gIsEndShow ) { + gIsEndShow = 0; + if ( base.msie > 0 && IsMac() ) + ChangeFrame( SLIDE_FRAME, GetHrefObj( g_currentSlide ).m_slideHref ); + else + PPTSld.history.back(); + + PPTNav.location.reload(); + if( PPTSld.event ) + PPTSld.event.cancelBubble=true; + } + else + base.GoToPrevSld(); +} +function M_True() { return true } +function M_False() { return false } + +function M_End() { + base.CloseFullScreen(); + /*PPTSld.event.cancelBubble=true; + window.close( self )*/ +} + +function CreateMenuItem( node,text,action,eval ) +{ + var e=CreateItem( node ) + e.type="menuitem" + e.Action=action + e.IsActive=eval + e.innerHTML=text + + if( !e.IsActive() ) + e.style.color="threedshadow" + e.onclick=Perform + e.onmouseover=Highlight + e.onmouseout=Deselect + s=e.style; + s.fontFamily=sFont + s.fontSize="8pt" + s.paddingLeft=2 +} +function CreateItem( node ) +{ + var elem=PPTSld.document.createElement("DIV") + node.insertBefore( elem ) + return elem +} +function SetCMBorder( o,ltClr,rbClr ) +{ + var s=o.style + s.backgroundColor="menu" + s.borderStyle="solid" + s.borderWidth=1 + s.borderColor=ltClr+" "+rbClr+" "+rbClr+" "+ltClr +} + +/* netscape context menu */ +g_ctxmenu = 0; +function setRect( obj, X, Y, W, H ) { + obj.top = Y; + obj.left = X; + obj.clip.top = 0; + obj.clip.left = 0; + obj.clip.bottom = H; + obj.clip.right = W; +} + +function KPH(event) { + if ( ! base.IsFullScrMode() && !alwaysOn ) + return true; + + if ( (!IsMac() &&event.which == 3) || ( IsMac() && (event.modifiers & Event.CONTROL_MASK) && event.which == 1 ) ) { + PPTSld.g_ctxmenu = 1; + PPTSld.stripUobj.visibility = "show"; + PPTSld.stripDobj.visibility = "show"; + PPTSld.shadeUobj.visibility = "show"; + PPTSld.shadeDobj.visibility = "show"; + PPTSld.panelobj.visibility = "show"; + PPTSld.Fobj.visibility = "show"; + PPTSld.Bobj.visibility = "show"; + PPTSld.Eobj.visibility = "show"; + + setRect(PPTSld.shadeUobj, event.pageX-2, event.pageY-2, 82, 67 ); + setRect(PPTSld.shadeDobj, event.pageX, event.pageY, 82, 67 ); + setRect(PPTSld.panelobj, event.pageX, event.pageY, 80, 65 ); + setRect(PPTSld.Fobj, event.pageX, event.pageY, 80, 20 ); + setRect(PPTSld.Bobj, event.pageX, event.pageY+20, 80, 20 ); + setRect(PPTSld.stripUobj, event.pageX, event.pageY+41, 80, 1 ); + setRect(PPTSld.stripDobj, event.pageX, event.pageY+43, 80, 1 ); + setRect(PPTSld.Eobj, event.pageX, event.pageY+45, 80, 20 ); + return false; + } + if ( HitOK( event ) ) { + PPTSld.g_ctxmenu = 0; + PPTSld.stripUobj.visibility = "hide"; + PPTSld.stripDobj.visibility = "hide"; + PPTSld.shadeUobj.visibility = "hide"; + PPTSld.shadeDobj.visibility = "hide"; + PPTSld.panelobj.visibility = "hide"; + PPTSld.Fobj.visibility = "hide"; + PPTSld.Bobj.visibility = "hide"; + PPTSld.Eobj.visibility = "hide"; + } + return true; +} + +function overMe() { + this.bgColor = "blue"; +} + +function outMe() { + this.bgColor = "#AAAAAA"; +} + +function makeElement( whichEl, whichContainer ) { + if ( arguments.length == 1 ) { + whichContainer = PPTSld; + } + tmp = new Layer(100,whichContainer); + eval( whichEl + " = tmp" ); + return eval(whichEl); +} + +function initMe( obj, clr, text ) { + obj.bgColor = clr; +// obj.document.write("<a href='javascript:return false'>" + text + "</a>"); + obj.document.write( "<font size=2 face=Arial " ); + if ( !M_HasPrevSld() && (obj == PPTSld.Bobj ) ) { + obj.document.write( " color='#808080' " ); + } + else { + obj.onmouseover = overMe; + obj.onmouseout = outMe; + } + obj.document.write( " >   " + text +"</font> <layer top=0 left=0 width=100 height=40 ></layer>"); + obj.document.close(); + obj.captureEvents(Event.CLICK); + obj.color = "black"; +} + +function createCM() { + if ( base.IsFullScrMode() ) { + var clr = "#AAAAAA"; + PPTSld.shadeUobj = makeElement("SHADEU"); + PPTSld.shadeDobj = makeElement("SHADED"); + PPTSld.panelobj = makeElement("PANEL"); + PPTSld.stripUobj = makeElement("STRIPU"); + PPTSld.stripDobj = makeElement("STRIPD"); + PPTSld.shadeUobj.bgColor = "#BBBBBB"; + PPTSld.shadeDobj.bgColor = "#888888"; + PPTSld.stripUobj.bgColor = "#777777"; + PPTSld.stripDobj.bgColor = "#CCCCCC"; + PPTSld.panelobj.bgColor = clr; + PPTSld.Fobj = makeElement("Next"); + PPTSld.Bobj = makeElement("Previous"); + PPTSld.Eobj = makeElement("EndShow"); + initMe( PPTSld.Fobj, clr, "Next" ); + PPTSld.Fobj.onclick = M_GoNextSld; + + initMe( PPTSld.Bobj, clr, "Previous" ); + PPTSld.Bobj.onclick = M_GoPrevSld; + + initMe( PPTSld.Eobj, clr, "End Show"); + PPTSld.Eobj.onclick = base.CloseFullScreen; + } +} + +function IsContextMenu() { + return (g_ctxmenu == 1) +} +var g_notesTable = new Array() +var g_hiddenSlide = new Array() +makeSlide( 0,1,1); +makeSlide( 1,1,1); +makeSlide( 2,1,1); +makeSlide( 3,1,1); +makeSlide( 4,1,1); +makeSlide( 5,1,1); +makeSlide( 6,1,1); +makeSlide( 7,1,1); +makeSlide( 8,1,1); +makeSlide( 9,1,1); +makeSlide( 10,1,1); +makeSlide( 11,0,1); +makeSlide( 12,0,1); +makeSlide( 13,1,1); + +var END_SHOW_HREF = "endshow.htm", + OUTLINE_EXPAND_HREF = "outline_expanded.htm", + OUTLINE_COLLAPSE_HREF = "outline_collapsed.htm", + OUTLINE_NAVBAR_HREF = "outline_navigation_bar.htm", + NAVBAR_HREF = "navigation_bar.htm", + BLANK_NOTES_HREF = "blank_notes.htm", + NUM_VISIBLE_SLIDES = 14, + SIMPLE_FRAMESET = 0, + SLIDE_FRAME = "PPTSld", + NOTES_FRAME = "PPTNts", + OUTLINE_FRAME = "PPTOtl", + OUTLINE_NAVBAR_FRAME = "PPTOtlNav", + NAVBAR_FRAME = "PPTNav", + MAIN_FRAME = "MainFrame", + FS_NAVBAR_HREF = "fs_navigation_bar.htm", + isIEFiles = 2, + isNAVFiles = 8, + isFLATFiles = 16, + includeNotes = 1, + PPTPRESENTATION = 1; +var INITSLIDENUM = 1; + +var EndSlideShow = 0; +var g_outline_href = OUTLINE_COLLAPSE_HREF; +var g_fullscrMode = 0; +var FSWin = null; +var gtmpstr = document.location.href; +var g_baseURL = gtmpstr.substr(0, gtmpstr.lastIndexOf("/") ) + "/" + "webqtl_demo2.ppt_files"; +var g_showoutline = 1; +var g_shownotes = includeNotes; +var g_currentSlide = INITSLIDENUM, g_prevSlide = INITSLIDENUM; +var saveFSSlideNum = saveTPSlideNum = g_currentSlide; +var saveFSprevSlide = saveTPprevSlide = g_prevSlide; +var g_slideType="ie"; +var appVer = navigator.appVersion; +var msie = appVer.indexOf( "MSIE " ) + appVer.indexOf( "Internet Explorer " ); +var isnav = ( navigator.appName.indexOf( "Netscape" ) >= 0 ); +var msieWin31 = (appVer.indexOf( "Windows 3.1" ) > 0); +var ver = 0; +var g_done = 0; +var g_prevotlobjidx = 0; +var g_ShowFSDefault = 0; +var g_lastVisibleSld = 1; +var g_allHidden = false; +function IsIE() { + return (msie >= 0 ); +} + +function IsNav() { + return (isnav); +} +var msiePos = appVer.indexOf( "MSIE " ); +var inexPos = appVer.indexOf( "Internet Explorer " ); +if ( msiePos >= 0 ) + ver = parseFloat( appVer.substring( msiePos+5, appVer.indexOf ( ";", msiePos ) ) ); +else if( inexPos >= 0 ) + ver=parseFloat( appVer.substring( inexPos+18, appVer.indexOf(";",inexPos) ) ) +else + ver = parseInt( appVer ); + +//var g_supportsPPTHTML = 0; //!msieWin31 && ( ( msie >= 0 && ver >= 3.02 ) || ( msie < 0 && ver >= 3 ) ); + +function GetCurrentSlideNum() +{ + obj = GetHrefObj( g_currentSlide ); + if ( GetHrefObj( g_currentSlide ).m_origVisibility == 1 ) + return obj.m_slideIdx; + else + return g_currentSlide; +} + +function GetNumSlides() +{ + if ( GetHrefObj( g_currentSlide ).m_origVisibility == 1 ) + return NUM_VISIBLE_SLIDES; + else + return g_docTable.length; +} + +function GetHrefObj( slideIdx ) +{ return g_docTable[slideIdx - 1]; +} + +function GetSlideNum( slideHref ) +{ + for (ii=0; ii<g_docTable.length; ii++) { + if ( g_docTable[ii].m_slideHref == slideHref ) + return ii+1; + } + return 1; +} + +function GoToNextSld() +{ + targetIdx = g_currentSlide + 1; + if ( GetHrefObj( targetIdx-1 ).m_origVisibility == 0 ) { + if ( targetIdx<=g_docTable.length ) { + obj = GetHrefObj( targetIdx ); + obj.m_visibility = 1; + GoToSld( obj.m_slideHref ); + } + } + else { + obj = GetHrefObj( targetIdx ); + while ( obj && ( obj.m_origVisibility == 0 ) && ( targetIdx<=g_docTable.length ) ) + obj = GetHrefObj( targetIdx++ ); + if( obj && obj.m_origVisibility ) + GoToSld( obj.m_slideHref ); + } +} + +function GoToPrevSld() +{ + targetIdx = g_currentSlide - 1; + if ( targetIdx > 0 ) { + obj = GetHrefObj( targetIdx ); + while ( ( obj.m_visibility == 0 ) && ( targetIdx>0 ) ) + obj = GetHrefObj( targetIdx-- ); + GoToSld( obj.m_slideHref ); + } +} + +function GoToLast() +{ + targetIdx = g_docTable.length; + if ( targetIdx != g_currentSlide ) + GoToSld( GetHrefObj( targetIdx ).m_slideHref ); +} + +function GoToFirst() +{ GoToSld( GetHrefObj(1).m_slideHref ); +} + +function highlite() { + if ( IsFullScrMode() ) + return; + index = GetCurrentSlideNum(); + if ( !frames[MAIN_FRAME].frames[OUTLINE_FRAME] ) + return; + if ( msie < 0 ) { + if ( g_prevotlobjidx != 0 ) { + eval( "otlobj = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.LAYERID" + g_prevotlobjidx ); + otlobj.hidden = true; + } + else + index = GetCurrentSlideNum(); + eval( "otlobj = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.LAYERID" + index ); + otlobj.hidden = false; + + g_prevotlobjidx = index; + + return; + } + if ( !g_showoutline ) + return; + + backclr = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.body.bgColor; + textclr = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.body.text; + if ( g_prevotlobjidx != 0 ) { + eval( "otlobj = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.all.p" + g_prevotlobjidx ); + otlobj.style.backgroundColor = backclr; + otlobj.style.color = textclr; + otlobj.all.AREF.style.color = textclr; + } + else + index = GetCurrentSlideNum(); + eval( "otlobj = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.all.p" + index ); + otlobj.style.backgroundColor = textclr; + otlobj.style.color = backclr; + otlobj.all.AREF.style.color = backclr; + g_prevotlobjidx = index; +} + +function ChangeFrame( frame, href ) +{ +if ( IsFramesMode() ) { + if ( NAVBAR_FRAME == frame || OUTLINE_NAVBAR_FRAME == frame ) { + frames[frame].location.replace(href); + } + else if( ! ( ( OUTLINE_FRAME == frame && !g_showoutline) || (NOTES_FRAME == frame && !g_shownotes ) ) ){ + frames[MAIN_FRAME].frames[frame].location.href = href; + } + } + else { + if ( frame == NAVBAR_FRAME || frame == SLIDE_FRAME ) { + if( frame == NAVBAR_FRAME ) { + href = FS_NAVBAR_HREF; + + } + if( frame == NAVBAR_FRAME ) + window.frames[frame].location.replace(href); + else + window.frames[frame].location.href = href; + } + } + +} + +function shutEventPropagation() { + if ( IsNav() ) + return; + + var slideFrame; + if ( IsFramesMode() ) + slideFrame = frames[MAIN_FRAME].frames[SLIDE_FRAME]; + else + slideFrame = window.frames[SLIDE_FRAME]; + if ( slideFrame.event ) + slideFrame.event.cancelBubble=true; +} + +function GoToSld( slideHref ) +{ + shutEventPropagation(); + if ( slideHref != GetHrefObj( g_currentSlide ).m_slideHref || g_slideType != GetHrefObj( g_currentSlide ).type) { + g_prevSlide = g_currentSlide; + g_currentSlide = GetSlideNum( slideHref ); + g_slideType = GetHrefObj( g_currentSlide ).type; + obj = GetHrefObj( g_currentSlide ); + obj.m_visibility = 1; + ChangeFrame( SLIDE_FRAME, slideHref ); + if( !SIMPLE_FRAMESET ) + ChangeFrame( NOTES_FRAME, obj.m_notesHref ); + ChangeFrame( NAVBAR_FRAME, NAVBAR_HREF ); + + } +} + +function PrevSldViewed() +{ GoToSld( GetHrefObj( g_prevSlide ).m_slideHref ); +} + +function NoHref() {} + +function ExpandOutline( ) +{ + g_outline_href = OUTLINE_EXPAND_HREF; + ChangeFrame( OUTLINE_FRAME, OUTLINE_EXPAND_HREF ); + frames[OUTLINE_NAVBAR_FRAME].location.replace( OUTLINE_NAVBAR_HREF); +} + +function CollapseOutline() +{ + g_outline_href = OUTLINE_COLLAPSE_HREF; + ChangeFrame( OUTLINE_FRAME, OUTLINE_COLLAPSE_HREF ); + frames[OUTLINE_NAVBAR_FRAME].location.replace( OUTLINE_NAVBAR_HREF); + } + +function SlideUpdated( id ) +{ + if ( id != GetHrefObj( g_currentSlide ).m_slideHref ) { + g_prevSlide = g_currentSlide; + g_currentSlide = GetSlideNum( id ); + obj = GetHrefObj( g_currentSlide ); + if( !SIMPLE_FRAMESET ) + ChangeFrame( NOTES_FRAME, obj.m_notesHref ); + ChangeFrame( NAVBAR_FRAME, NAVBAR_HREF ); + } +} + +function hrefList( slideHref, notesHref, visible, slideIdx, type ) +{ + this.m_slideHref = slideHref; + this.m_notesHref = notesHref; + this.m_navbarHref = NAVBAR_HREF; + this.m_origVisibility = visible; + this.m_visibility = visible; + this.m_slideIdx = slideIdx; + this.type = type; +} + +function IsFullScrMode() { + return g_fullscrMode; +} + + +function IsFramesMode() { + return (1 - g_fullscrMode); +} + +function SldUpdated( id ) +{ + if ( ( id != GetHrefObj( g_currentSlide ).m_slideHref ) || ( g_currentSlide == g_lastVisibleSld ) ){ + g_prevSlide = g_currentSlide; + g_currentSlide = GetSlideNum( id ); + obj = GetHrefObj( g_currentSlide ); + if( !SIMPLE_FRAMESET ) + ChangeFrame( NOTES_FRAME, obj.m_notesHref ); + ChangeFrame( NAVBAR_FRAME, NAVBAR_HREF ); + } +} + +function ToggleOutline() { + g_showoutline = 1 - g_showoutline; + writeMyFrame(); +} + +function ShowHideNotes() { + g_shownotes = 1 - g_shownotes; + writeMyFrame(); +} + +function writeMyFrame() { + SetFSMode(0); + obj = frames[MAIN_FRAME]; + + var curslide = g_baseURL + "/" + GetHrefObj( g_currentSlide ).m_slideHref; + var curnotes = g_baseURL + "/" + GetHrefObj( g_currentSlide ).m_notesHref; + var otlhref = g_baseURL + "/" + g_outline_href; + if ( msie < 0 ) { + if ( ! g_showoutline && g_shownotes ) { + obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \ + <frameset rows=\"*,20%\" id=\"frameset2\" > \ + <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \ + <frame src=\"' + curnotes + '\" name=PPTNts marginheight=0 marginwidth=0> \ + </frameset> </html>' ); + } + else if( g_showoutline && g_shownotes ){ + obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \ + <frameset cols=\"20%,*\" id=\"frameset1\"> \ + <frame src=\"' + otlhref + '\" name=PPTOtl> \ + <frameset rows=\"*,20%\" id=\"frameset2\" > \ + <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \ + <frame src=\"' + curnotes + '\" name=PPTNts marginheight=0 marginwidth=0> \ + </frameset> </frameset></html>' ); + } + else if ( !g_shownotes && !g_showoutline ) { + obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \ + <frameset rows="*,0" frameborder=0 > \ + <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \ + </frameset> </html>' ); + } + else if( !g_shownotes && g_showoutline ) { + obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \ + <frameset cols=\"20%,*\" id=\"frameset1\"> \ + <frame src=\"' + otlhref + '\" name=PPTOtl> \ + <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \ + </frameset></html>' ); + } + obj.document.close(); + } + else { + if ( g_showoutline ) { + obj.PPTHorizAdjust.cols = "20%,*"; + obj.PPTOtl.location.reload(); + } + else { + obj.PPTHorizAdjust.cols = "0,*"; + } + if ( g_shownotes ) { + obj.PPTVertAdjust.rows = "*,20%"; + obj.PPTNts.location.href = curnotes; + } + else { + obj.PPTVertAdjust.rows = "*,0"; + } + } + ChangeFrame( OUTLINE_NAVBAR_FRAME, OUTLINE_NAVBAR_HREF ); +} + +function FullScreen() { + g_done = 0; + + + SetFSMode(1); + if ( msie >= 0 ) + FSWin = window.open( g_baseURL + "/" + "fullscreen.htm", null, "fullscreen=yes"); + else { + var height = screen.availHeight; + if ( window.navigator.platform.indexOf( "Mac" ) >= 0 ) { + height -= 30; + } + FSWin = window.open( g_baseURL + "/" + "fullscreen.htm", "null", "height="+ height + ",width=" + screen.availWidth + ",screenX=0,screenY=0"); + } +} + +function SetFSMode( i ) { + +} + +function Slide( i ) { + SetFSMode(0); + GoToSld(GetHrefObj(i).m_slideHref); +} + +function TP_GoToNextSld() { + SetFSMode(0); + GoToNextSld(); +} + +function TP_GoToPrevSld() { + SetFSMode(0); + GoToPrevSld(); +} + +function CloseFullScreen() { + g_done = 0; + + if ( IsNav() ){ + if ( self.opener ) + opener.FSWin = null; + } + window.close(); +} + +function slidenum(i) { + var slidename = "slide"; + if ( i < 10 ) + return ( slidename + "000" + i); + else if ( i < 100 ) + return ( slidename + "00" + i ); + else if ( i < 1000 ) + return (slidename + "0" + i ); + else + return (slidename + i ); +} +function UpdateLastVisibleSlide( index ) { + if ( g_lastVisibleSld < index ) + g_lastVisibleSld = index; +} + +function jpegArray( numSlides ) { +count_hidden = 0; + g_docTable = new Array(); + for( i=0; i<numSlides; i++ ) { + j = 2 * numSlides + i + 1; + var str = slidenum( j ) +".htm"; + if( g_notesTable[i] == 1 ) + g_docTable[i] = new hrefList( str, slidenum(i+1 ) + "_notes_pane.htm", g_hiddenSlide[i], i+1-count_hidden, "jpeg" ); + else + g_docTable[i] = new hrefList( str, BLANK_NOTES_HREF, g_hiddenSlide[i], i+1-count_hidden, "jpeg" ); + if ( !g_hiddenSlide[i] ) count_hidden++; + else UpdateLastVisibleSlide( i+1 ); + } +} + +function ieArray( numSlides ) { +count_hidden = 0; + g_docTable = new Array(); + for( i=0; i<numSlides; i++ ) { + var str = slidenum(i+1) +".htm"; + if( g_notesTable[i] == 1 ) + g_docTable[i] = new hrefList( str, slidenum( i+1 ) + "_notes_pane.htm", g_hiddenSlide[i], i+1-count_hidden, "ie" ); + else + g_docTable[i] = new hrefList( str, BLANK_NOTES_HREF, g_hiddenSlide[i], i+1-count_hidden, "ie" ); + if ( !g_hiddenSlide[i] ) count_hidden++; + else UpdateLastVisibleSlide( i+1 ); + } +} + +function navArray( numSlides ) { +count_hidden = 0; + g_docTable = new Array(); + for( i=0; i<numSlides; i++ ) { + j = numSlides + i + 1; + var str = slidenum( j ) +".htm"; + if( g_notesTable[i] == 1 ) + g_docTable[i] = new hrefList( str, slidenum(i+1 ) + "_notes_pane.htm", g_hiddenSlide[i], i+1-count_hidden, "nav" ); + else + g_docTable[i] = new hrefList( str, BLANK_NOTES_HREF, g_hiddenSlide[i], i+1-count_hidden, "nav" ); + if ( !g_hiddenSlide[i] ) count_hidden++; + else UpdateLastVisibleSlide( i+1 ); + } +} + +function LoadHTMLVersion() { + var os = window.navigator.platform.indexOf("Mac"); + if ( (msie || isnav ) && ( (os < 0 && ver >= 4 ) || ( os >= 0 && ver >= 5 ) || (os >=0 && msie < 0 && ver >= 4 ) ) ){ + if ( msie >= 0 ) { + if ( isIEFiles > 0 ) + ieArray( 14 ); + else if ( isFLATFiles > 0 ){ + /*if ( IsFramesMode() ) + StatusPlay("This presentation is optimized for use with older versions of your browser. Since you are using a more recent version of Microsoft Internet Explorer or Netscape Navigator, consider optimizing this presentation to take advantage of your current version's advanced capabilities."); */ + jpegArray( 14 ); + } + else + window.location.replace( "webqtl_demo2.ppt_files/error.htm" ); + } + else { + if ( isNAVFiles > 0 && ver < 5) + navArray( 14 ); + else if ( isFLATFiles > 0 ) { + /* if ( IsFramesMode() ) + StatusPlay("This presentation is optimized for use with older versions of your browser. Since you are using a more recent version of Microsoft Internet Explorer or Netscape Navigator, consider optimizing this presentation to take advantage of your current version's advanced capabilities."); */ + jpegArray( 14 ); + } + else + window.location.replace( "webqtl_demo2.ppt_files/error.htm" ); + } +} +else { + /* + if ( IsFramesMode() && !isWebTV() ) + StatusPlay("This presentation contains content that your browser may not be able to show properly. This presentation was optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator."); + */ + if ( isFLATFiles <= 0 ) { + /* if ( IsFramesMode() ) + window.alert("This presentation contains content that your browser may not be able to display properly. This presentation is optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator." ); + */ + window.location.replace( "webqtl_demo2.ppt_files/error.htm" ); + } + /* + else if ( IsFramesMode() && !isWebTV() ) + StatusPlay( "This presentation contains content that your browser may not be able to show properly. This presentation was optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator." ); + */ + jpegArray ( 14 ); + } + +} + +function isWebTV() { + if ( window.navigator.appName.indexOf( 'WebTV' ) >= 0 ) + return true; + return false; +} + +var count; +var statusText; +var statusfirst = 0; + function display50( text ) +{ + len = text.length; + if ( len < 50 && count < 2) { + window.status = text; + window.setTimeout( "repeat()", 300 ); + } + else { + var period = 200; + window.status = text; + newtext = text.substring( 1, len ); + if ( statusfirst ) { + statusfirst = 0; + period = 2000; + } + window.setTimeout( "display50( newtext )", period ); + } +} +function repeat( ) { + count++; + statusfirst = 1; + display50( statusText ); +} + +function StatusPlay( text ) { + count = 0; + statusText = text; + repeat( ); + } +function makeSlide( i, notes, visible ) { + g_notesTable[i] = notes; + g_hiddenSlide[i] = visible; +} + diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001.htm new file mode 100755 index 00000000..11938baa --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: The GeneNetwork and WebQTL : PART 2 link to www.genenetwork.org"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0001.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:3.53%;left:2.11%;width:96.15%;height:18.19%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-277 0 -1";mso-margin-left-alt:232; mso-text-indent-alt:0;position:absolute;top:11.65%;left:.96%;width:98.2%; height:73.78%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size:73%'>The GeneNetwork and WebQTL : PART 2<span style="mso-spacerun: yes"> </span><br> </span></span><span style='position:absolute;top:48.68%;left:4.34%;width:95.23%'><span style='font-size:73%'>link to www.genenetwork.org</span><span style='font-size: 73%;mso-special-format:lastCR;display:none'><i><br> </i></span></span></div> </div> <div style='position:absolute;top:24.02%;left:5.82%;width:54.03%;height:68.55%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='position:absolute;top:0%;left:3.67%;width:96.32%; height:61.34%'> <div style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:0%;left:0%;width:100.0%;height:51.68%'><span style='position:absolute;top:0%;left:0%;width:89.05%'><span style='mso-special-format: nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size: 99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part 1. How to study </span></span><span style='position:absolute;top:23.57%; left:9.66%;width:79.13%'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>expression variation </span></span><span style='position:absolute; top:47.15%;left:9.66%;width:90.33%'><span style='font-size:94%;color:#E9EB5D; mso-color-index:3'>and genetic correlation </span></span><span style='position:absolute;top:70.73%;left:9.66%;width:79.13%'><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>(slides 2–17)<br> </span></span></div> <div style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:60.5%;left:0%;width:93.63%;height:39.91%'><span style='position:absolute;top:0%;left:0%;width:95.1%'><span style='mso-special-format: nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size: 99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part 2. Discovering </span></span><span style='position:absolute;top:30.52%; left:10.32%;width:89.67%'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>upstream modulators </span></span><span style='position:absolute;top:61.05%; left:10.32%;width:84.51%'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>(slides 18–29)</span></span></div> </div> </div> <img border=0 src="slide0001_image001.png" style='position:absolute;top:17.84%; left:74.17%;width:23.57%;height:64.31%'> <div class=O style='position:absolute;top:75.44%;left:74.56%;width:10.46%; height:14.48%'> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:42.68%'><span style='font-family:"Arial Rounded MT Bold";font-size:233%;color:#6E6E6E'>RNA</span><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; display:none'><br> </span></div> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:45.12%;left:0%;width:82.27%;height:54.87%'><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; mso-special-format:lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:82.15%;left:4.1%;width:96.15%;height:18.19%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'></div> <img border=0 src="slide0001_image002.png" style='position:absolute;top:50.53%; left:48.74%;width:25.56%;height:13.07%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Part 2: Discovering upstream modulators and quantitative trait loci (QTLs). A quantitative trait locus is a chromosomal region that harbors one or a few polymorphic gene loci that influence a trait. We are going to be looking for QTLs that modulate the steady state expression level of App in the adult mouse forebrain.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_image001.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_image001.png new file mode 100755 index 00000000..a1cb20e4 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_image001.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_image002.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_image002.png new file mode 100755 index 00000000..e06bd0db --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_image002.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_notes_pane.htm new file mode 100755 index 00000000..9e0445f3 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Part 2: Discovering upstream modulators and quantitative trait loci (QTLs). A quantitative trait locus is a chromosomal region that harbors one or a few polymorphic gene loci that influence a trait. We are going to be looking for QTLs that modulate the steady state expression level of App in the adult mouse forebrain.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0002.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0002.htm new file mode 100755 index 00000000..b40dd6e1 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0002.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master05_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0002.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master05_background.png" v:shapes="_x0000_s3075" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div class=O style='position:absolute;top:92.93%;left:8.74%;width:18.67%; height:5.83%'> <div style='mso-line-spacing:"-134 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.48%'><span style='font-family:Times;font-size:117%;color:white;display:none'><br> </span></div> <div style='mso-line-spacing:"-134 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.51%;left:0%;width:100.0%;height:48.48%'><span style='font-family:Times;font-size:117%;color:white;mso-special-format:lastCR; display:none'><br> </span></div> </div> <div class=O style='position:absolute;top:92.93%;left:35.49%;width:29.4%; height:5.83%'> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:48.48%'><span style='font-family:Times;font-size:117%;color:white; display:none'><br> </span></div> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:51.51%;left:0%;width:100.0%; height:48.48%'><span style='font-family:Times;font-size:117%;color:white; mso-special-format:lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:2.12%;left:-5.43%;width:105.96%;height:11.13%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:0%;left:0%;width:100.0%;height:92.06%'> <div style='text-align:center;mso-line-spacing:"-240 0 0";mso-margin-left-alt: 16;mso-text-indent-alt:16;position:absolute;top:0%;left:0%;width:100.0%; height:65.51%'><span style='font-family:Arial;font-size:267%;color:#E9EB5D'>How to make recombinant inbred strains (RI)</span><span style='font-family:Arial; font-size:150%;color:aqua;display:none'><br> </span></div> <div style='text-align:center;mso-line-spacing:"-160 0 0";mso-margin-left-alt: 16;mso-text-indent-alt:16;position:absolute;top:62.06%;left:6.37%;width:87.37%; height:37.93%'><span style='font-family:Arial;font-size:150%;color:aqua; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <img border=0 src="slide0002_image003.png" style='position:absolute;top:28.79%; left:45.43%;width:18.14%;height:1.06%'><img border=0 src="slide0002_image004.png" style='position:absolute;top:20.31%;left:28.21%; width:1.98%;height:11.83%'> <div style='position:absolute;top:15.01%;left:25.03%;width:19.47%;height:9.71%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:9.09%;left:6.8%;width:93.19%; height:81.81%'> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>C57BL/6J (B)<br> </span></div> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:83.21%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <img border=0 src="slide0002_image005.png" style='position:absolute;top:20.31%; left:30.46%;width:1.98%;height:11.83%'> <div style='position:absolute;top:15.01%;left:62.25%;width:16.55%;height:9.71%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:9.09%;left:8.0%;width:92.8%; height:81.81%'> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>DBA/2J (D)<br> </span></div> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:82.75%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <img border=0 src="slide0002_image006.png" style='position:absolute;top:20.31%; left:66.62%;width:4.23%;height:11.83%'><img border=0 src="slide0002_image007.png" style='position:absolute;top:35.51%;left:23.97%; width:50.86%;height:1.23%'><img border=0 src="slide0002_image008.png" style='position:absolute;top:35.68%;left:24.1%;width:.66%;height:4.06%'><img border=0 src="slide0002_image009.png" style='position:absolute;top:35.68%; left:40.92%;width:.52%;height:4.06%'><img border=0 src="slide0002_image010.png" style='position:absolute;top:35.68%;left:57.61%;width:.52%;height:4.06%'><img border=0 src="slide0002_image011.png" style='position:absolute;top:35.68%; left:74.3%;width:.52%;height:3.88%'> <div style='position:absolute;top:42.75%;left:5.69%;width:6.49%;height:12.36%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:8.57%;left:20.4%;width:73.46%; height:84.28%'> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:49.15%'><span style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F1<br> </b></span></div> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:50.84%;left:0%;width:83.33%;height:49.15%'><span style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format:lastCR; display:none'><b><br> </b></span></div> </div> </div> <img border=0 src="slide0002_image012.png" style='position:absolute;top:39.92%; left:22.25%;width:4.23%;height:11.83%'><img border=0 src="slide0002_image013.png" style='position:absolute;top:39.92%;left:38.94%; width:4.23%;height:11.83%'><img border=0 src="slide0002_image014.png" style='position:absolute;top:39.92%;left:55.62%;width:4.23%;height:11.83%'><img border=0 src="slide0002_image015.png" style='position:absolute;top:39.39%; left:72.84%;width:4.23%;height:11.83%'><img border=0 src="slide0002_image016.png" style='position:absolute;top:43.46%;left:43.97%; width:11.12%;height:3.53%'><img border=0 src="slide0002_image017.png" style='position:absolute;top:60.95%;left:20.66%;width:9.8%;height:3.53%'> <div style='position:absolute;top:71.73%;left:58.41%;width:20.26%;height:26.67%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:12.58%;left:6.53%;width:88.23%; height:83.44%'> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:69.84%'><span style='position:absolute;top:0%;left:0%;width:99.25%'><span style='font-family:Arial;font-size:117%;color:#FFFF99'><b>20 generations </b></span></span><span style='position:absolute;top:39.77%;left:0%;width:100.0%'><span style='font-family:Arial;font-size:117%;color:#FFFF99'><b>brother-sister </b></span></span><span style='position:absolute;top:80.68%;left:0%;width:99.25%'><span style='font-family:Arial;font-size:117%;color:#FFFF99'><b>matings</b></span><span style='font-family:Arial;font-size:233%;color:#FFFF99;display:none'><b><br> </b></span></span></div> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:73.8%;left:0%;width:99.25%; height:26.98%'><span style='font-family:Arial;font-size:233%;color:#FFFF99; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> </div> <img border=0 src="slide0002_image018.png" style='position:absolute;top:60.95%; left:50.72%;width:9.93%;height:3.53%'><img border=0 src="slide0002_image019.png" style='position:absolute;top:62.72%;left:54.03%;width:4.37%;height:28.97%'><img border=0 src="slide0002_image020.png" style='position:absolute;top:61.13%; left:79.86%;width:10.86%;height:3.53%'><img border=0 src="slide0002_image021.png" style='position:absolute;top:62.36%;left:83.97%; width:4.1%;height:28.79%'> <div style='position:absolute;top:92.93%;left:21.72%;width:9.27%;height:9.71%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:9.09%;left:12.85%;width:85.71%; height:81.81%'> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD1</span><span style='font-family:Arial;font-size:150%;color:#484848;display:none'><br> </span></div> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:83.33%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#484848;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:92.75%;left:51.78%;width:9.27%;height:9.71%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:9.09%;left:12.85%;width:85.71%; height:81.81%'> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD2<br> </span></div> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:83.33%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:92.93%;left:80.79%;width:10.99%;height:5.65%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:15.62%;left:12.04%;width:87.95%; height:68.75%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD80</span></div> </div> <div style='position:absolute;top:90.45%;left:64.1%;width:17.74%;height:17.49%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:6.06%;left:7.46%;width:92.53%; height:88.88%'> <div style='mso-line-spacing:"-341 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.86%'><span style='font-family:Arial;font-size:300%;color:#FFFF99'>+ É +<br> </span></div> <div style='mso-line-spacing:"-341 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:50.0%;left:0%;width:83.87%;height:48.86%'><span style='font-family:Arial;font-size:300%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:62.89%;left:4.9%;width:6.49%;height:12.36%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:7.14%;left:20.4%;width:73.46%; height:84.28%'> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:49.15%'><span style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F2<br> </b></span></div> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:50.84%;left:0%;width:83.33%;height:49.15%'><span style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format:lastCR; display:none'><b><br> </b></span></div> </div> </div> <img border=0 src="slide0002_image022.png" style='position:absolute;top:54.24%; left:18.01%;width:75.62%;height:1.06%'><img border=0 src="slide0002_image023.png" style='position:absolute;top:54.06%;left:17.88%; width:.66%;height:3.88%'><img border=0 src="slide0002_image024.png" style='position:absolute;top:54.24%;left:32.45%;width:.52%;height:3.88%'><img border=0 src="slide0002_image025.png" style='position:absolute;top:54.24%; left:48.07%;width:.52%;height:4.06%'><img border=0 src="slide0002_image026.png" style='position:absolute;top:54.24%;left:62.78%;width:.52%;height:4.06%'><img border=0 src="slide0002_image027.png" style='position:absolute;top:54.24%; left:77.74%;width:.52%;height:4.06%'><img border=0 src="slide0002_image028.png" style='position:absolute;top:54.59%;left:92.71%;width:.52%;height:3.71%'><img border=0 src="slide0002_image029.png" style='position:absolute;top:44.87%; left:49.13%;width:.79%;height:10.07%'><img border=0 src="slide0002_image030.png" style='position:absolute;top:57.59%;left:15.89%;width:4.23%;height:11.83%'><img border=0 src="slide0002_image031.png" style='position:absolute;top:57.59%; left:30.86%;width:4.37%;height:11.83%'><img border=0 src="slide0002_image032.png" style='position:absolute;top:57.59%;left:46.35%; width:4.23%;height:11.83%'><img border=0 src="slide0002_image033.png" style='position:absolute;top:57.59%;left:60.92%;width:4.23%;height:11.83%'><img border=0 src="slide0002_image034.png" style='position:absolute;top:57.59%; left:75.62%;width:4.23%;height:11.83%'><img border=0 src="slide0002_image035.png" style='position:absolute;top:57.59%;left:90.86%; width:4.23%;height:11.83%'><img border=0 src="slide0002_image036.png" style='position:absolute;top:84.09%;left:56.42%;width:1.98%;height:1.41%'><img border=0 src="slide0002_image037.png" style='position:absolute;top:80.21%; left:25.96%;width:1.98%;height:11.83%'><img border=0 src="slide0002_image038.png" style='position:absolute;top:84.98%;left:86.09%; width:1.85%;height:2.12%'> <div style='position:absolute;top:75.61%;left:1.58%;width:13.9%;height:13.78%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:7.69%;left:.95%;width:99.04%; height:85.89%'> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:7.69%;width:83.65%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'><b>BXD RI<br> </b></span></div> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:32.83%;left:0%;width:100.0%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'><b>Strain set<br> </b></span></div> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:67.16%;left:7.69%;width:83.65%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> </div> <img border=0 src="slide0002_image039.png" style='position:absolute;top:12.36%; left:14.17%;width:10.59%;height:6.36%'><img border=0 src="slide0002_image040.png" style='position:absolute;top:10.6%;left:76.42%; width:14.3%;height:8.3%'> <div style='position:absolute;top:20.84%;left:17.48%;width:9.53%;height:13.78%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:7.69%;left:6.94%;width:88.88%; height:85.89%'> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:7.81%;width:82.81%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>fully<br> </span></div> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:32.83%;left:0%;width:100.0%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>inbred<br> </span></div> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:67.16%;left:7.81%;width:82.81%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:38.16%;left:2.91%;width:11.78%;height:9.71%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:9.09%;left:3.37%;width:94.38%; height:81.81%'> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>isogenic<br> </span></div> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:51.11%;left:8.33%;width:83.33%; height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:54.41%;left:1.85%;width:12.18%;height:13.78%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:7.69%;left:2.17%;width:95.65%; height:85.89%'> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:7.95%;width:84.09%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>hetero-<br> </span></div> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:32.83%;left:0%;width:100.0%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>geneous<br> </span></div> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:67.16%;left:7.95%;width:84.09%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:74.91%;left:29.0%;width:21.98%;height:21.73%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:4.06%;left:5.42%;width:89.15%; height:91.86%'> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:79.64%'><span style='position:absolute;top:0%;left:.67%;width:99.32%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>Recombined </span></span><span style='position:absolute;top:25.55%;left:.67%;width:99.32%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>chromosomes </span></span><span style='position:absolute;top:51.11%;left:0%;width:100.0%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>are needed for </span></span><span style='position:absolute;top:75.55%;left:.67%;width:99.32%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>mapping<br> </span></span></div> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:80.53%;left:.67%;width:99.32%; height:19.46%'><span style='font-family:Arial;font-size:150%;color:#FFFF99; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:10.24%;left:25.56%;width:10.46%;height:9.71%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:9.09%;left:12.65%;width:87.34%; height:81.81%'> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>female<br> </span></div> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:84.05%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:10.24%;left:64.5%;width:7.94%;height:9.71%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:9.09%;left:15.0%;width:83.33%; height:81.81%'> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>male<br> </span></div> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:84.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:30.56%;left:78.01%;width:19.47%;height:9.71%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:16.36%;left:6.12%;width:93.19%; height:74.54%'> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:41.46%'><span style='font-family:Arial;font-size:117%;color:#FFFF99'>chromosome pair</span><span style='font-family:Arial;font-size:150%;color:#FFFF99;display:none'><br> </span></div> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:46.34%;left:0%;width:83.21%;height:53.65%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <img border=0 src="slide0002_image041.png" style='position:absolute;top:31.09%; left:65.82%;width:12.84%;height:2.82%'> <div style='position:absolute;top:86.21%;left:3.97%;width:9.8%;height:14.13%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:5.0%;left:5.4%;width:90.54%; height:87.5%'> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:8.95%;width:82.08%; height:24.28%'><span style='font-family:Arial;font-size:117%;color:#E9EB5D'>Inbred<br> </span></div> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:25.71%;left:0%;width:100.0%; height:24.28%'><span style='font-family:Arial;font-size:117%;color:#E9EB5D'>Isogenic<br> </span></div> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:50.0%;left:4.47%;width:89.55%; height:24.28%'><span style='font-family:Arial;font-size:117%;color:#E9EB5D'>siblings</span><span style='font-family:Arial;font-size:117%;color:aqua;display:none'><br> </span></div> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:75.71%;left:8.95%;width:82.08%; height:24.28%'><span style='font-family:Arial;font-size:117%;color:aqua; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <img border=0 src="slide0002_image042.png" style='position:absolute;top:79.32%; left:83.84%;width:1.98%;height:11.83%'><img border=0 src="slide0002_image043.png" style='position:absolute;top:84.8%;left:83.7%; width:1.85%;height:2.12%'><img border=0 src="slide0002_image044.png" style='position:absolute;top:79.85%;left:53.5%;width:1.98%;height:11.83%'><img border=0 src="slide0002_image045.png" style='position:absolute;top:83.92%; left:53.5%;width:1.98%;height:1.41%'><img border=0 src="slide0002_image046.png" style='position:absolute;top:80.21%;left:23.44%;width:1.98%;height:11.83%'> <div style='position:absolute;top:18.72%;left:43.04%;width:13.77%;height:9.54%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='mso-line-spacing:"-341 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:11.11%;left:9.61%;width:90.38%; height:79.62%'><span style='font-family:Arial;font-size:300%;color:aqua'>B</span><span style='font-family:Arial;font-size:300%;color:#FFFF99'>X</span><span style='font-family:Arial;font-size:300%;color:#FF1911'>D</span></div> </div> <img border=0 src="slide0002_image047.png" style='position:absolute;top:27.2%; left:32.98%;width:31.39%;height:4.06%'><img border=0 src="slide0002_image048.png" style='position:absolute;top:66.25%;left:60.92%; width:1.98%;height:3.18%'><img border=0 src="slide0002_image049.png" style='position:absolute;top:64.31%;left:15.89%;width:1.98%;height:5.3%'><img border=0 src="slide0002_image050.png" style='position:absolute;top:57.59%; left:75.62%;width:1.98%;height:5.65%'><img border=0 src="slide0002_image051.png" style='position:absolute;top:28.44%;left:48.87%;width:.92%;height:8.12%'><img border=0 src="slide0002_image052.png" style='position:absolute;top:62.19%; left:23.84%;width:3.57%;height:16.96%'><img border=0 src="slide0002_image053.png" style='position:absolute;top:61.48%;left:63.17%; width:1.98%;height:8.12%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The next few slides provide a short introduction to mapping the loci that are responsible for variation in a trait such as App expression level. These modulatory regions of the genome are sometimes called quantitative trait loci or QTLs. You may want to do some independent reading on this topic if this is your first exposure to QTL analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The genetic reference population (GRP) of BXD recombinant inbred strains were originally generated about 25 years ago by Benjamin Taylor at The Jackson Laboratory. He crossed female C57BL/6J mice with male DBA/2J mice to generate the F1 and F2 progeny. At the bottom of this slide we have schematized one chromosome pair from three of the BXD RI strains.<span style="mso-spacerun: yes"> </span>The dashed vertical lines that lead to the final BXD RI lines involve 21 full sib matings (about 7 years of breeding). Some lines die out during inbreeding. For example, there is no longer any BXD3 strain.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. Over the last decade, our group (Lu Lu and Rob Williams) and Jeremy Peirce and Lee Silver at Princeton have enlarged Ben TaylorÕs set. There are now just over 80 BXD strains. They have all been genotyped using about 13,700 markers (SNPs and microsatellites). These markers are used to define the ÒblueÓ and ÒredÓ regions of the chromosomes as shown in the figure above.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. Chromosomes of RI GRPs usually have about 4 times as many recombinations as those of F2 animals. However, unlike an F2, both chromosomes of an RI are identical. Therefore, 50 RI strains contain as many recombinations as 100 F2 animals.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. BXD43 through BXD100 were generated using a special method that resulted in a further doubling of the average recombination density per chromosome. 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+</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The next few slides provide a short introduction to mapping the loci that are responsible for variation in a trait such as App expression level. These modulatory regions of the genome are sometimes called quantitative trait loci or QTLs. You may want to do some independent reading on this topic if this is your first exposure to QTL analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The genetic reference population (GRP) of BXD recombinant inbred strains were originally generated about 25 years ago by Benjamin Taylor at The Jackson Laboratory. He crossed female C57BL/6J mice with male DBA/2J mice to generate the F1 and F2 progeny. At the bottom of this slide we have schematized one chromosome pair from three of the BXD RI strains.<span style="mso-spacerun: yes"> </span>The dashed vertical lines that lead to the final BXD RI lines involve 21 full sib matings (about 7 years of breeding). Some lines die out during inbreeding. For example, there is no longer any BXD3 strain.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>1. Over the last decade, our group (Lu Lu and Rob Williams) and Jeremy Peirce and Lee Silver at Princeton have enlarged Ben TaylorÕs set. There are now just over 80 BXD strains. They have all been genotyped using about 13,700 markers (SNPs and microsatellites). These markers are used to define the ÒblueÓ and ÒredÓ regions of the chromosomes as shown in the figure above.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2. Chromosomes of RI GRPs usually have about 4 times as many recombinations as those of F2 animals. However, unlike an F2, both chromosomes of an RI are identical. Therefore, 50 RI strains contain as many recombinations as 100 F2 animals.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>3. BXD43 through BXD100 were generated using a special method that resulted in a further doubling of the average recombination density per chromosome. The entire set of 80 BXDs therefore contains as many recombinations as about 260 F2 animals.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003.htm new file mode 100755 index 00000000..2c4a0620 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0003.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img border=0 src="slide0003_image054.png" style='position:absolute;top:40.45%; left:73.24%;width:14.56%;height:5.3%'> <div class=O style='position:absolute;top:40.81%;left:74.56%;width:11.92%; height:7.24%'> <div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:60.97%'><span style='font-family:Gadget;font-size:150%;color:white'>aa<br> </span></div> <div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:41.46%;left:0%;width:100.0%;height:60.97%'><span style='font-family:Gadget;font-size:150%;color:white;mso-special-format:lastCR; display:none'><br> </span></div> </div> <img border=0 src="slide0003_image055.png" style='position:absolute;top:16.6%; left:73.24%;width:14.56%;height:5.3%'> <div class=O style='position:absolute;top:16.96%;left:74.56%;width:11.92%; height:7.24%'> <div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:60.97%'><span style='font-family:Gadget;font-size:150%;color:white'>aaaa<br> </span></div> <div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:41.46%;left:0%;width:100.0%;height:60.97%'><span style='font-family:Gadget;font-size:150%;color:white;mso-special-format:lastCR; display:none'><br> </span></div> </div> <div style='position:absolute;top:20.31%;left:71.65%;width:25.96%;height:19.43%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:10.0%;left:5.1%;width:95.4%; height:84.54%'> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:45.16%'><span style='font-size:267%;color:#E2EBF0'>D2 strain</span><span style='font-family: Palatino;font-size:333%;color:#FBFDB8;display:none'><br> </span></div> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:49.46%;left:0%;width:88.77%;height:50.53%'><span style='font-family:Palatino;font-size:333%;color:#FBFDB8;mso-special-format: lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:43.81%;left:71.65%;width:25.56%;height:19.43%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:10.9%;left:5.18%;width:94.81%; height:84.54%'> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:45.16%'><span style='font-size:267%;color:#F6BF69'>B6 strain</span><span style='font-family: Palatino;font-size:333%;color:#F6BF69;display:none'><br> </span></div> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:48.38%;left:0%;width:87.43%;height:50.53%'><span style='font-family:Palatino;font-size:333%;color:#F6BF69;mso-special-format: lastCR;display:none'><br> </span></div> </div> </div> <img border=0 src="slide0003_image056.png" style='position:absolute;top:17.31%; left:31.25%;width:1.32%;height:42.22%'><img border=0 src="slide0003_image057.png" style='position:absolute;top:40.63%;left:31.39%; width:39.86%;height:3.53%'> <div style='position:absolute;top:20.67%;left:38.27%;width:30.19%;height:26.32%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:6.04%;left:4.38%;width:92.1%; height:89.93%'> <div style='mso-line-spacing:"-320 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:58.2%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size: 233%;color:#E9EB5D'><i>amount of </i></span></span><span style='position:absolute; top:53.84%;left:0%;width:100.0%'><span style='font-size:233%;color:#E9EB5D'><i>transcript</i></span><span style='font-family:Palatino;font-size:367%;color:#E9EB5D;display:none'><br> </span></span></div> <div style='mso-line-spacing:"-422 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:61.19%;left:0%;width:100.0%;height:38.8%'><span style='font-family:Palatino;font-size:367%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:6.0%;left:72.45%;width:21.05%;height:19.43%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:10.0%;left:6.28%;width:88.67%; height:84.54%'> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:45.16%'><span style='font-size:267%;color:white'>4 </span><span style='font-size:233%; color:white'>units</span><span style='font-family:Palatino;font-size:333%; color:#E9EB5D;display:none'><br> </span></div> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:49.46%;left:0%;width:100.0%;height:50.53%'><span style='font-family:Palatino;font-size:333%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:29.5%;left:72.45%;width:21.05%;height:19.43%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:10.9%;left:6.28%;width:88.67%; height:84.54%'> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:45.16%'><span style='font-size:267%;color:white'>2</span><span style='font-size:233%; color:white'> units</span><span style='font-family:Palatino;font-size:333%; color:#E9EB5D;display:none'><br> </span></div> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:48.38%;left:0%;width:100.0%;height:50.53%'><span style='font-family:Palatino;font-size:333%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </div> </div> <img border=0 src="slide0003_image058.png" style='position:absolute;top:15.72%; left:31.25%;width:40.26%;height:5.47%'> <div class=O style='position:absolute;top:17.84%;left:9.93%;width:4.76%; height:16.43%'> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#E2EBF0'>D<br> </span></div> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:49.46%;left:0%;width:83.33%;height:50.53%'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR;display:none'><br> </span></div> </div> <div class=O style='position:absolute;top:17.84%;left:17.88%;width:4.23%; height:16.43%'> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#F6BF69'>B<br> </span></div> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:49.46%;left:0%;width:84.37%;height:50.53%'><span style='font-size:300%;color:#F6BF69;mso-special-format:lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:79.5%;left:5.43%;width:104.1%;height:13.6%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='mso-line-spacing:"-256 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:3.89%;left:1.27%;width:98.72%; height:93.5%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size:233%;color:#E2EBF0'>D</span><span style='font-size:233%; color:#E9EB5D'> </span><span style='font-size:200%;color:#E9EB5D'>and </span><span style='font-size:233%;color:#F6BF69'>B</span><span style='font-size:233%; color:#E9EB5D'> </span><span style='font-size:200%;color:#E9EB5D'>may be SNP-like variants in the promoter </span></span><span style='position:absolute; top:34.72%;left:0%;width:99.74%'><span style='font-size:200%;color:#E9EB5D'>itself (cis QTL) or in </span><span style='font-size:200%;color:#EAEC5E'>upstream genes (trans QTLs)</span><span style='font-size:300%;color:#E9EB5D'>.</span></span></div> </div> <div class=O style='position:absolute;top:7.59%;left:4.23%;width:22.78%; height:16.25%'> <div style='text-align:center;mso-line-spacing:"-233 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:1.74%;width:97.09%; height:33.69%'><span style='font-size:200%;color:#E9EB5D'>UPSTREAM<br> </span></div> <div style='text-align:center;mso-line-spacing:"-233 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:32.6%;left:0%;width:100.0%; height:33.69%'><span style='font-size:200%;color:#E9EB5D'>modulators<br> </span></div> <div style='text-align:center;mso-line-spacing:"-233 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:66.3%;left:4.65%;width:90.69%; height:33.69%'><span style='font-size:200%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:7.59%;left:44.5%;width:16.95%;height:17.84%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:3.96%;left:7.03%;width:85.15%; height:92.07%'> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#E2EBF0'>High<br> </span></div> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:49.46%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:63.78%;left:8.74%;width:6.35%;height:17.84%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='position:absolute;top:3.96%;left:20.83%;width:75.0%; height:92.07%'> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#E2EBF0'>D<br> </span></div> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:49.46%;left:0%;width:83.33%;height:50.53%'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:63.78%;left:15.09%;width:5.96%;height:17.84%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='position:absolute;top:3.96%;left:20.0%;width:71.11%; height:92.07%'> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#F6BF69'>B<br> </span></div> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:49.46%;left:0%;width:84.37%;height:50.53%'><span style='font-size:300%;color:#F6BF69;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:71.02%;left:7.54%;width:16.02%;height:12.54%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='position:absolute;top:5.63%;left:7.43%;width:91.73%; height:87.32%'> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.0%'><span style='font-size:200%;color:#E9EB5D'><i>cis QTL</i></span><span style='font-size:200%;color:#E9EB5D;display:none'><br> </span></div> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:48.38%;left:0%;width:82.88%;height:50.0%'><span style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <img border=0 src="slide0003_image059.png" style='position:absolute;top:57.24%; left:-1.05%;width:101.98%;height:7.59%'> <div class=O style='position:absolute;top:44.16%;left:47.15%;width:9.4%; height:12.72%'> <div style='mso-line-spacing:"-272 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:51.38%'><span style='font-size:233%;color:#F6BF69'>Low<br> </span></div> <div style='mso-line-spacing:"-272 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:50.0%;left:0%;width:83.09%;height:51.38%'><span style='font-size:233%;color:#F6BF69;mso-special-format:lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:58.12%;left:.79%;width:113.37%;height:6.36%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='mso-line-spacing:"-200 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:11.11%;left:1.16%;width:98.83%; height:75.0%'><span style='font-family:Gadget;font-size:167%;color:white'>>>>>PROMOTER--ATG-Exon1-Intron1-Exon2-Intron2 - etc-3'UTR >>>>></span></div> </div> <img border=0 src="slide0003_image060.png" style='position:absolute;top:37.98%; left:8.6%;width:13.77%;height:20.67%'> <div class=O style='position:absolute;top:40.28%;left:10.99%;width:1.72%; height:11.48%'> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:46.15%'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:50.76%;left:7.69%;width:84.61%; height:50.76%'><span style='font-family:Palatino;font-size:233%;color:white; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> <div class=O style='position:absolute;top:40.63%;left:18.41%;width:1.72%; height:11.48%'> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:46.15%'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:49.23%;left:7.69%;width:84.61%; height:50.76%'><span style='font-family:Palatino;font-size:233%;color:white; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> <img border=0 src="slide0003_image061.png" style='position:absolute;top:33.74%; left:8.6%;width:13.77%;height:20.67%'> <div class=O style='position:absolute;top:36.39%;left:18.41%;width:1.72%; height:11.48%'> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:46.15%'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:49.23%;left:7.69%;width:84.61%; height:50.76%'><span style='font-family:Palatino;font-size:233%;color:white; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> <div class=O style='position:absolute;top:36.04%;left:10.99%;width:1.72%; height:11.48%'> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:46.15%'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:49.23%;left:7.69%;width:84.61%; height:50.76%'><span style='font-family:Palatino;font-size:233%;color:white; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> <div class=O style='position:absolute;top:37.8%;left:20.66%;width:.13%; height:12.01%'> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white; display:none'><b><br> </b></span></div> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:51.47%;left:0%;width:100.0%; height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> <img border=0 src="slide0003_image062.png" style='position:absolute;top:27.38%; left:4.9%;width:21.45%;height:21.37%'> <div style='position:absolute;top:27.38%;left:5.03%;width:20.92%;height:12.54%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='position:absolute;top:5.63%;left:6.32%;width:94.3%; height:87.32%'> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.0%'><span style='font-size:200%;color:#E9EB5D'><i>trans QTL</i></span><span style='font-size:200%;color:#E9EB5D;display:none'><br> </span></div> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:48.38%;left:0%;width:83.22%;height:50.0%'><span style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>This slide is illustrates two major types of QTLs that modulate variability in transcript-relative steady state abundance.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. cis QTLs are defined as QTLs that are closely linked to the gene whose transcript is the measured trait. For example, a polymorphism in the promoter that affects binding of a transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms in enhancers or may be in 3Õ UTR binding sites that affect message stability.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. trans QTLs map far enough away from the location of the gene that gives rise to the transcript that is being measured so that we can be fairly certain that the QTL is not in the gene itself. The most blatant type of trans QTL would be a polymorphism in a transcription factor. But in the majority of cases, the trans QTLs can be far removed in a mechanistic sense from the actual events modulating transcript abundance. That is why there are three overlapping arrows in the figure.<span style="mso-spacerun: yes"> </span>The way in which an upstream polymorphism influences a downstream difference in mRNA abundance can be indirect. Effects can:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>a.<span style="mso-spacerun: yes"> </span>cross tissue types (a polymorphic liver enzyme may affect CNS gene expression)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>b.<span style="mso-spacerun: yes"> </span>cross time (the modulator is only expressed for one day during development but has permanent effects in adults)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>c.<span style="mso-spacerun: yes"> </span>may be contingent on environmental factors (heat shock may trigger the expression of a polymorphic factor that affects mRNA abundance).</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003_image005.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003_image005.png new file mode 100755 index 00000000..d1370484 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003_image005.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003_image006.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003_image006.png new file mode 100755 index 00000000..c9843a48 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003_image006.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003_image008.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003_image008.png new file mode 100755 index 00000000..504177df --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003_image008.png Binary files differdiff --git 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b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003_image062.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003_notes_pane.htm new file mode 100755 index 00000000..68c0fb55 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>This slide is illustrates two major types of QTLs that modulate variability in transcript-relative steady state abundance.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>1. cis QTLs are defined as QTLs that are closely linked to the gene whose transcript is the measured trait. For example, a polymorphism in the promoter that affects binding of a transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms in enhancers or may be in 3Õ UTR binding sites that affect message stability.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. trans QTLs map far enough away from the location of the gene that gives rise to the transcript that is being measured so that we can be fairly certain that the QTL is not in the gene itself. The most blatant type of trans QTL would be a polymorphism in a transcription factor. But in the majority of cases, the trans QTLs can be far removed in a mechanistic sense from the actual events modulating transcript abundance. That is why there are three overlapping arrows in the figure.<span style="mso-spacerun: yes"> </span>The way in which an upstream polymorphism influences a downstream difference in mRNA abundance can be indirect. Effects can:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2><span style="mso-spacerun: yes"> </span>a.<span style="mso-spacerun: yes"> </span>cross tissue types (a polymorphic liver enzyme may affect CNS gene expression)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2><span style="mso-spacerun: yes"> </span>b.<span style="mso-spacerun: yes"> </span>cross time (the modulator is only expressed for one day during development but has permanent effects in adults)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2><span style="mso-spacerun: yes"> </span>c.<span style="mso-spacerun: yes"> </span>may be contingent on environmental factors (heat shock may trigger the expression of a polymorphic factor that affects mRNA abundance).</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004.htm new file mode 100755 index 00000000..8f72f910 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Discovering upstream modulatory loci"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0004.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img border=0 src="slide0004_image063.png" style='position:absolute;top:38.86%; left:5.03%;width:84.9%;height:45.75%'> <div style='position:absolute;top:5.47%;left:2.51%;width:93.64%;height:8.65%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-358 0 -1";position:absolute;top:20.4%; left:1.41%;width:97.31%;height:75.51%'><span style='font-family:Verdana; font-size:64%'>Discovering upstream modulatory loci</span><span style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display: none'><i><br> </i></span></div> </div> <img border=0 src="slide0004_image064.png" style='position:absolute;top:20.31%; left:18.01%;width:19.2%;height:25.97%'><img border=0 src="slide0004_image065.png" style='position:absolute;top:32.5%;left:78.01%; width:19.2%;height:25.97%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Please bring the Trait Data and Analysis window to the front and look for the Interval Mapping button. Confirm that you are back to the trait amyloid beta precursor protein.<span style="mso-spacerun: yes"> </span>If so, then just click the button.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notice that the default for:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Select Chrs (chromosomes) is ALL</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Select Mapping Scale is set to GENETIC</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Options: Permutation test YES<span style="mso-spacerun: yes"> </span>(2000 is the default number)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Options: Bootstrap test YES (2000 is the default number)</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image010.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image010.png new file mode 100755 index 00000000..08c136e3 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image010.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image012.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image012.png new file mode 100755 index 00000000..b8e67f4d --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image012.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image063.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image063.png new file mode 100755 index 00000000..891bc06c --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image063.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image064.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image064.png new file mode 100755 index 00000000..8905caa6 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image064.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image065.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image065.png new file mode 100755 index 00000000..7f5a5295 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image065.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_notes_pane.htm new file mode 100755 index 00000000..b1988954 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Please bring the Trait Data and Analysis window to the front and look for the Interval Mapping button. Confirm that you are back to the trait amyloid beta precursor protein.<span style="mso-spacerun: yes"> </span>If so, then just click the button.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Notice that the default for:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Select Chrs (chromosomes) is ALL</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Select Mapping Scale is set to GENETIC</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Options: Permutation test YES<span style="mso-spacerun: yes"> </span>(2000 is the default number)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Options: Bootstrap test YES (2000 is the default number)</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005.htm new file mode 100755 index 00000000..b2dc8582 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: WebQTL searches for upstream controllers"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0005.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:-.53%;left:1.72%;width:101.19%;height:8.65%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;position:absolute;top:18.36%;left:.91%;width:98.95%; height:75.51%'><span style='font-family:Verdana;font-size:64%'><i>WebQTL searches for upstream controllers</i></span><span style='font-family:Verdana; font-size:73%;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </div> <div style='position:absolute;top:71.02%;left:34.96%;width:45.96%;height:19.78%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:3.57%;left:2.3%;width:97.69%; height:91.96%'><span style='position:absolute;top:0%;left:0%;width:98.82%'><span style='font-size:167%;color:#E9EB5D'><i>App maps on Chr 16 (blue </i></span></span><span style='position:absolute;top:25.24%;left:0%;width:100.0%'><span style='font-size:167%;color:#E9EB5D'><i>arrow points to the orange </i></span></span><span style='position:absolute;top:49.51%;left:0%;width:86.72%'><span style='font-size:167%;color:#E9EB5D'><i>triangle) but the best </i></span></span><span style='position:absolute;top:74.75%;left:0%;width:86.72%'><span style='font-size:167%;color:#E9EB5D'><i>locus is on Chr 7.</i></span><span style='font-size:233%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></div> </div> <img border=0 src="slide0005_image066.png" style='position:absolute;top:8.83%; left:1.19%;width:98.27%;height:53.88%'><img border=0 src="slide0005_image067.png" style='position:absolute;top:46.64%;left:15.76%; width:15.89%;height:53.35%'><img border=0 src="slide0005_image068.png" style='position:absolute;top:46.64%;left:80.0%;width:10.99%;height:53.35%'><img border=0 src="slide0005_image069.png" style='position:absolute;top:41.34%; left:76.02%;width:11.65%;height:22.79%'><img border=0 src="slide0005_image070.png" style='position:absolute;top:41.51%;left:29.13%; width:12.71%;height:24.38%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>This is a major output type: a so-called full-genome interval map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The X-axis represents all 19 autosomes and the X chromosome as if they were laid end to end with short gaps between the telomere of one chromosome and the centromere of the next chromosome (mouse chromosomes only have a single long arm and the centromere represents the origin of each chromosome for numerical purpose: 0 centimorgans at almost 0 megabases). The blue labels along the bottom of the figure list a subset of the 3795 markers that were used in mapping.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The thick blue wavy line running across chromosomes summarizes the strength of association between variation in the phenotype (App expression differences) and the two genotypes of all markers and the intervals between markers (hence, interval mapping).<span style="mso-spacerun: yes"> </span>The height of the wave (blue Y-axis to the left) provides the likelihood ratio statistic (LRS). Divide by 4.61 to convert these values to LOD scores.<span style="mso-spacerun: yes"> </span>Or you can read them as a chi-square-like statistic.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The red line and the red axis to the far right provide an estimate of the effect that a QTL has on expression of App (this estimate of the so-called additive effect tends to be too high). If the red line is below the X-axis then this means that the allele inherited from C57BL/6J (B6 or B) at a particular marker is associated with higher values. If the red line is above the X-axis then the DBA/2J allele (D2 or D) is associated with higher trait values. Multiply the additive effect size by 2 to estimate the difference between the set of strains that have the B/B genotype and those that have the D/D genotype at a specific marker. For example, on distal Chr 7 the red line peaks at a value of about 0.2. That means that this region of chromosome 2 is responsible for a 0.4 unit expression difference between B/B strains and the D/D strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The yellow histogram bars: These summarize the results of a whole-genome bootstrap of the trait that is performed 1000 times. What is a bootstrap? A bootstrap provides a method to evaluate whether results are robust. If we drop out one strain, do we still get the same results? When mapping quantitative traits, each strain normally gets one equally weighted vote. But using the bootstrap procedure, we give each strain a random weighting factor of between 0 and 1.<span style="mso-spacerun: yes"> </span>We then remap the trait and find THE SINGLE BEST LRS VALUE per bootstrap. We do this 1000 times. In this example, most bootstrap results cluster on Chr 3 and Chr 7 under the LRS peaks. That is somewhat reassuring. But notice that a substantial number of bootstrap are scattered around on other chromosomes. About 30% of the bootstrap resamples have a peak on Chr 7. That is pretty good, but does makes us realize that the sample we are working with is still quite small and fragile.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The horizontal dashed lines at 10.5 and 17.3 are the likelihood ratio statistic (LRS) values associated with the suggestive and significant genome-wide probabilities that were established by permutations of phenotypes across genotypes. We shuffle randomly 2000 times and obtain a distribution of peak LRS scores to generate a null distribution. Five percent of the time, one of these permuted data sets will have a peak LRS higher than 17.3. We call that level the 0.05 significance threshold for a whole genome scan. The p = 0.67 point is the suggestive level, and corresponds to the green dashed line.<span style="mso-spacerun: yes"> </span>These thresholds are conservative for transcripts that have expression variation that is highly heritable. The putative or suggestive QTL on Chr 3 is probably more than just suggestive.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>One other point: the mapping procedure we use is computationally very fast, but it is relatively simple. We are not looking for gene-gene interactions and we are not fitting multiple QTLs in combinations. Consider this QTL analysis a first pass that will highlight hot spots and warm spots that are worth following up on using more sophisticated models.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>CLICKABLE REGIONS:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. If you click on the Chromosome number then you will generate a new map just for that chromosome.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. If you click on the body of the map, say on the blue line, then you will generate a view on a 10 Mb window of that part of the genome from the UCSC Genome Browser web site.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. If you click on a marker symbol, then you will generate a new Trait data and Analysis window with the genotypes loaded into the window just like any other trait. More on this in Section 3.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>4. You can drag these maps off of the browser window and onto your desktop. They will be saved as PNG or PDF files. You can import them into Photoshop or other programs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>5. There is also an option at the bottom of the page to download a 2X higher resolution image of this plot for papers and presentations.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>6. You can also download the results of the analysis in a text format</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image013.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image013.png new file mode 100755 index 00000000..55769e36 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image013.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image014.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image014.png new file mode 100755 index 00000000..e49ba16e --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image014.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image066.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image066.png new file mode 100755 index 00000000..5ab7794c --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image066.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image067.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image067.png new file mode 100755 index 00000000..c26d4792 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image067.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image068.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image068.png new file mode 100755 index 00000000..af0745a5 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image068.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image069.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image069.png new file mode 100755 index 00000000..6ec88720 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image069.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image070.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image070.png new file mode 100755 index 00000000..9c156ddc --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image070.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_notes_pane.htm new file mode 100755 index 00000000..279e38cf --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>This is a major output type: a so-called full-genome interval map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The X-axis represents all 19 autosomes and the X chromosome as if they were laid end to end with short gaps between the telomere of one chromosome and the centromere of the next chromosome (mouse chromosomes only have a single long arm and the centromere represents the origin of each chromosome for numerical purpose: 0 centimorgans at almost 0 megabases). The blue labels along the bottom of the figure list a subset of the 3795 markers that were used in mapping.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The thick blue wavy line running across chromosomes summarizes the strength of association between variation in the phenotype (App expression differences) and the two genotypes of all markers and the intervals between markers (hence, interval mapping).<span style="mso-spacerun: yes"> </span>The height of the wave (blue Y-axis to the left) provides the likelihood ratio statistic (LRS). Divide by 4.61 to convert these values to LOD scores.<span style="mso-spacerun: yes"> </span>Or you can read them as a chi-square-like statistic.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The red line and the red axis to the far right provide an estimate of the effect that a QTL has on expression of App (this estimate of the so-called additive effect tends to be too high). If the red line is below the X-axis then this means that the allele inherited from C57BL/6J (B6 or B) at a particular marker is associated with higher values. If the red line is above the X-axis then the DBA/2J allele (D2 or D) is associated with higher trait values. Multiply the additive effect size by 2 to estimate the difference between the set of strains that have the B/B genotype and those that have the D/D genotype at a specific marker. For example, on distal Chr 7 the red line peaks at a value of about 0.2. That means that this region of chromosome 2 is responsible for a 0.4 unit expression difference between B/B strains and the D/D strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The yellow histogram bars: These summarize the results of a whole-genome bootstrap of the trait that is performed 1000 times. What is a bootstrap? A bootstrap provides a method to evaluate whether results are robust. If we drop out one strain, do we still get the same results? When mapping quantitative traits, each strain normally gets one equally weighted vote. But using the bootstrap procedure, we give each strain a random weighting factor of between 0 and 1.<span style="mso-spacerun: yes"> </span>We then remap the trait and find THE SINGLE BEST LRS VALUE per bootstrap. We do this 1000 times. In this example, most bootstrap results cluster on Chr 3 and Chr 7 under the LRS peaks. That is somewhat reassuring. But notice that a substantial number of bootstrap are scattered around on other chromosomes. About 30% of the bootstrap resamples have a peak on Chr 7. That is pretty good, but does makes us realize that the sample we are working with is still quite small and fragile.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The horizontal dashed lines at 10.5 and 17.3 are the likelihood ratio statistic (LRS) values associated with the suggestive and significant genome-wide probabilities that were established by permutations of phenotypes across genotypes. We shuffle randomly 2000 times and obtain a distribution of peak LRS scores to generate a null distribution. Five percent of the time, one of these permuted data sets will have a peak LRS higher than 17.3. We call that level the 0.05 significance threshold for a whole genome scan. The p = 0.67 point is the suggestive level, and corresponds to the green dashed line.<span style="mso-spacerun: yes"> </span>These thresholds are conservative for transcripts that have expression variation that is highly heritable. The putative or suggestive QTL on Chr 3 is probably more than just suggestive.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>One other point: the mapping procedure we use is computationally very fast, but it is relatively simple. We are not looking for gene-gene interactions and we are not fitting multiple QTLs in combinations. Consider this QTL analysis a first pass that will highlight hot spots and warm spots that are worth following up on using more sophisticated models.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>CLICKABLE REGIONS:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>1. If you click on the Chromosome number then you will generate a new map just for that chromosome.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2. If you click on the body of the map, say on the blue line, then you will generate a view on a 10 Mb window of that part of the genome from the UCSC Genome Browser web site.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>3. If you click on a marker symbol, then you will generate a new Trait data and Analysis window with the genotypes loaded into the window just like any other trait. More on this in Section 3.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>4. You can drag these maps off of the browser window and onto your desktop. They will be saved as PNG or PDF files. You can import them into Photoshop or other programs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>5. There is also an option at the bottom of the page to download a 2X higher resolution image of this plot for papers and presentations.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>6. You can also download the results of the analysis in a text format</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006.htm new file mode 100755 index 00000000..f647c55a --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Genetic versus Physical maps for App expression"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0006.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:-.53%;left:1.72%;width:116.02%;height:8.65%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;position:absolute;top:18.36%;left:.79%;width:99.2%; height:75.51%'><span style='font-family:Verdana;font-size:64%'><i>Genetic versus Physical maps for App expression</i></span><span style='font-family: Verdana;font-size:73%;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </div> <img border=0 src="slide0006_image071.png" style='position:absolute;top:8.83%; left:1.72%;width:98.27%;height:39.92%'><img border=0 src="slide0006_image072.png" style='position:absolute;top:35.51%;left:1.85%; width:98.27%;height:54.06%'> <div class=O style='position:absolute;top:91.69%;left:5.96%;width:95.23%; height:7.42%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size:117%;color:#E9EB5D'><i>The difference between genetic and physical scale is analogous to measuring the </i></span></span><span style='position:absolute;top:42.85%;left:0%;width:96.66%'><span style='font-size:117%;color:#E9EB5D'><i>separation between New York and Boston in either travel hours or kilometers</i></span><span style='font-size:150%; color:#E9EB5D'><i>.</i></span><span style='font-size:167%;color:#E9EB5D; mso-special-format:lastCR;display:none'><i><br> </i></span></span></div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The map on the top has an X-axis scale based on frequency of recombinations events between markers (B to D transitions, see slide 19 for a color-coded example). These so-called genetic maps are scaled in centimorgan (recombinations per 100 gametes). In contrast, the physical map shown below the genetic map has an X-axis scale based on DNA length measured in nucleotides or base-pairs. Notice the large difference between the two maps in the size of Chr 19 (large on the genetic scale but small on the physical scale).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Also notice the large difference in the width of the chromosome 7 QTL peak. In mice, recombinations occur with higher frequency toward the telomeric side (right side) of each chromosome. As a result, genetic maps are stretched out more toward the telomere relative to a physical map. The QTL on distal Chr 7 is therefore actually more precisely mapped than might appear looking at the genetic map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The physical scale is becoming more useful than the genetic scale primarily because many other data types can be easily superimposed on a physical map. You will see more examples in the next several slides.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image015.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image015.png new file mode 100755 index 00000000..ff7d776a --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image015.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image071.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image071.png new file mode 100755 index 00000000..0e63f836 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image071.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image072.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image072.png new file mode 100755 index 00000000..3c44c2ab --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image072.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_notes_pane.htm new file mode 100755 index 00000000..c1f7d244 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The map on the top has an X-axis scale based on frequency of recombinations events between markers (B to D transitions, see slide 19 for a color-coded example). These so-called genetic maps are scaled in centimorgan (recombinations per 100 gametes). In contrast, the physical map shown below the genetic map has an X-axis scale based on DNA length measured in nucleotides or base-pairs. Notice the large difference between the two maps in the size of Chr 19 (large on the genetic scale but small on the physical scale).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Also notice the large difference in the width of the chromosome 7 QTL peak. In mice, recombinations occur with higher frequency toward the telomeric side (right side) of each chromosome. As a result, genetic maps are stretched out more toward the telomere relative to a physical map. The QTL on distal Chr 7 is therefore actually more precisely mapped than might appear looking at the genetic map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The physical scale is becoming more useful than the genetic scale primarily because many other data types can be easily superimposed on a physical map. You will see more examples in the next several slides.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007.htm new file mode 100755 index 00000000..01fb76a9 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Physical map for distal chromosome 7"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0007.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:-.53%;left:1.72%;width:101.05%;height:8.65%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;position:absolute;top:18.36%;left:.91%;width:97.9%; height:75.51%'><span style='font-family:Verdana;font-size:64%'>Physical map for distal chromosome 7</span><span style='font-family:Verdana;font-size:73%; mso-special-format:lastCR;display:none'><i><br> </i></span></div> </div> <div style='position:absolute;top:7.77%;left:5.82%;width:94.03%;height:6.18%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:11.42%;left:1.12%;width:98.87%; height:74.28%'><span style='font-size:167%;color:#E9EB5D'>Distal Chr 7 from ~120 and 132 Mb may modulate</span><span style='font-size:167%;color:#E9EB5D'><i> App</i></span><span style='font-size:200%;color:#E9EB5D;mso-special-format: lastCR;display:none'><i><br> </i></span></div> </div> <img border=0 src="slide0007_image073.png" style='position:absolute;top:93.28%; left:6.62%;width:75.23%;height:3.71%'><img border=0 src="slide0007_image075.png" style='position:absolute;top:15.54%;left:6.62%;width:68.34%;height:75.61%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Physical map of variation in App expression in brain on distal Chr 7 (a blow up of the whole-genome map on the previous slide).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Verdana size=3> You can now see that the X-axis is on a physical scale of megabases (Mb). The QTL peak is roughly between 120 and 132 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. The small irregular colored blocks and marks toward the top of the map mark the locations of genes superimposed on the physical map. Neighboring genes are offset slightly in the vertical axis for display purpose. Note one region of very high gene density from about 120 to 123 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. The orange hash marks along the X-axis represent the number of single nucleotide polymorphisms that distinguish the two parental strains (C57BL/6J and DBA/2J) from each other. We call this the SNP seismograph track (see Glossary for more details). Regions with low numbers of SNPs have closely matched sequences and are less likely to contain QTLs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>4. As before, the thin red line shows the additive effect size. By convention the positive values signify the D alleles are associated with higher expression of App in this region of Chr 7 than the B alleles. The maximum effect size is about +0.20 log2 expression units per D allele. The differences been the BB and DD genotypes (BB and DD because each strain has two alleles; one per chromosome) is therefore about 2^0.4 = 1.32 or a 32% increment in DD relative to BB at this locus.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>5. If you scroll just under the Physical Map you will see text that reads ÒDISPLAY from XXX Mb TO YYY MbÉ..Ó<span style="mso-spacerun: yes"> </span>These physical maps are zoomable, a feature we will exploit to evaluate candidate genes in this QTL interval.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image016.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image016.png new file mode 100755 index 00000000..53a17c76 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image016.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image017.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image017.png new file mode 100755 index 00000000..308c4df0 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image017.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image073.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image073.png new file mode 100755 index 00000000..c0174c3f --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image073.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image075.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image075.png new file mode 100755 index 00000000..9a3e3264 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image075.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_notes_pane.htm new file mode 100755 index 00000000..24c42724 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Physical map of variation in App expression in brain on distal Chr 7 (a blow up of the whole-genome map on the previous slide).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Verdana size=2> You can now see that the X-axis is on a physical scale of megabases (Mb). The QTL peak is roughly between 120 and 132 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2. The small irregular colored blocks and marks toward the top of the map mark the locations of genes superimposed on the physical map. Neighboring genes are offset slightly in the vertical axis for display purpose. Note one region of very high gene density from about 120 to 123 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>3. The orange hash marks along the X-axis represent the number of single nucleotide polymorphisms that distinguish the two parental strains (C57BL/6J and DBA/2J) from each other. We call this the SNP seismograph track (see Glossary for more details). Regions with low numbers of SNPs have closely matched sequences and are less likely to contain QTLs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>4. As before, the thin red line shows the additive effect size. By convention the positive values signify the D alleles are associated with higher expression of App in this region of Chr 7 than the B alleles. The maximum effect size is about +0.20 log2 expression units per D allele. The differences been the BB and DD genotypes (BB and DD because each strain has two alleles; one per chromosome) is therefore about 2^0.4 = 1.32 or a 32% increment in DD relative to BB at this locus.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>5. If you scroll just under the Physical Map you will see text that reads ÒDISPLAY from XXX Mb TO YYY MbÉ..Ó<span style="mso-spacerun: yes"> </span>These physical maps are zoomable, a feature we will exploit to evaluate candidate genes in this QTL interval.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008.htm new file mode 100755 index 00000000..8a9290b6 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Evaluating candidate genes"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0008.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img border=0 src="slide0008_image076.png" style='position:absolute;top:34.09%; left:1.72%;width:97.48%;height:61.48%'> <div style='position:absolute;top:-1.06%;left:.79%;width:93.64%;height:8.65%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-358 0 -1";position:absolute;top:18.36%; left:1.41%;width:97.31%;height:75.51%'><span style='font-family:Verdana; font-size:64%'>Evaluating candidate genes</span><span style='font-family:Verdana; font-size:73%;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </div> <img border=0 src="slide0008_image077.png" style='position:absolute;top:8.83%; left:1.72%;width:34.83%;height:22.61%'> <div style='position:absolute;top:3.35%;left:69.53%;width:33.9%;height:17.84%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:3.96%;left:2.73%;width:93.75%; height:91.08%'> <div style='text-align:center;position:absolute;top:0%;left:0%;width:100.0%; height:33.69%'><span style='font-size:200%;color:#E9EB5D'><i>Right position<br> </i></span></div> <div style='text-align:center;position:absolute;top:32.6%;left:0%;width:100.0%; height:67.39%'><span style='position:absolute;top:0%;left:.41%;width:100.0%'><span style='font-size:200%;color:#E9EB5D'><i>and high </i></span></span><span style='position:absolute;top:50.0%;left:0%;width:100.0%'><span style='font-size:200%;color:#E9EB5D'><i>correlation</i></span></span></div> </div> </div> <div style='position:absolute;top:17.84%;left:75.89%;width:21.72%;height:14.31%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:3.7%;left:0%;width:100.0%;height: 88.88%'> <div style='text-align:center;position:absolute;top:0%;left:6.7%;width:86.58%; height:58.33%'><span style='font-size:267%;color:#E9EB5D'><i><span style="mso-spacerun: yes"> </span></i></span><span style='font-size:200%; color:#E9EB5D'><i>= better<br> </i></span></div> <div style='text-align:center;position:absolute;top:56.94%;left:0%;width:100.0%; height:43.05%'><span style='font-size:200%;color:#E9EB5D'><i>candidates</i></span></div> </div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4><b>Evaluating candidate genes (CHECKED BOXES) responsible for variability in APP expression:</b></font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>A large number of genes are usually in the QTL interval and are therefore POSITIONAL CANDIDATES, but they will differ greatly in their biological and bioinformatic plausibility. Assume that the QTL has been located between 119 and 131 Mb (12 Mb). There will typically be 12 to 15 genes per Mb, so we might need to evaluate several hundred positional candidates. In this particular case there are about 100 known genes in this interval. Eight of these are highlighted in the table above with check marks in the boxes to the left.<span style="mso-spacerun: yes"> </span>We need to highlight and objectively score the biologically relevant subset of all 100 positional candidate genes. We could look through gene ontologies and expression levels to help us shorten the list. An alternate way available using WebQTL is to generate a list of those genes in this interval that have transcripts that co-vary in expression with App expression. That is what the table shows.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. To replicate this table go back to the Trait Data and Analysis Form. Choose to sort correlations by POSITION and select RETURN = 500. Then scroll down the list to Chr 7 and review the subset of positional candidates that share expression with App. You should see a list similar to that shown above. Gtf3c1 is a good biological candidate and has a high covariation in expression with App.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>2. Caveat:<span style="mso-spacerun: yes"> </span>Of course, the gene or genes that control App expression may not be in this list. A protein coding difference might be the ultimate cause of variation in App transcript level and the expression covariation might be close to zero. Our list may also simply be missing the right transcript since the microarray is not truly comprehensive. Furthermore, even if the list contains the QTL gene, an expression difference may only have been expressed early in development or even in another tissue such as liver. While it is important to recognize these caveats, it is equally important to devise a rational way to rank candidates given existing data. Coexpression is one of several criteria used to evaluate positional candidates. We will see others in the next slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>3. We can also assess the likelihood that candidates contain functional polymorphism in promoters and enhancers that affect their expression simply by mapping the transcripts of all candidate genes to see if they Òmap backÓ to the location of gene itself. A transcript that maps to its own location is referred to as a cis QTL. We essentially ask: Which of the transcripts listed in the Correlation Table above (from Gtf3c1 to Zranb1) has variation in expression that maps to Chr 7 at about 120 Mb?<span style="mso-spacerun: yes"> </span>The logic of this search is that if a gene controls the level of its own expression it is also much more likely to generate other downstream effects. The Gtf3c1 transcript is a weak cis QTL with a local LRS maximum of about 7.0 (D alleles are high). That is just about sufficient to declare it to be a cis QTL. [No whole genome correction is required and a point-wise p-value of 0.05 is the appropriate test. A p-value of 0.05 is roughly equivalent to an LRS of 6.0 (LOD = 1.3).]</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image018.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image018.png new file mode 100755 index 00000000..9535e6bb --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image018.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image019.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image019.png new file mode 100755 index 00000000..7e86d735 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image019.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image021.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image021.png new file mode 100755 index 00000000..2f8dfb0a --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image021.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image076.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image076.png new file mode 100755 index 00000000..14e3fbe5 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image076.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image077.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image077.png new file mode 100755 index 00000000..ec9fff87 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image077.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_notes_pane.htm new file mode 100755 index 00000000..9f5e373a --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4><b>Evaluating candidate genes (CHECKED BOXES) responsible for variability in APP expression:</b></font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>A large number of genes are usually in the QTL interval and are therefore POSITIONAL CANDIDATES, but they will differ greatly in their biological and bioinformatic plausibility. Assume that the QTL has been located between 119 and 131 Mb (12 Mb). There will typically be 12 to 15 genes per Mb, so we might need to evaluate several hundred positional candidates. In this particular case there are about 100 known genes in this interval. Eight of these are highlighted in the table above with check marks in the boxes to the left.<span style="mso-spacerun: yes"> </span>We need to highlight and objectively score the biologically relevant subset of all 100 positional candidate genes. We could look through gene ontologies and expression levels to help us shorten the list. An alternate way available using WebQTL is to generate a list of those genes in this interval that have transcripts that co-vary in expression with App expression. That is what the table shows.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. To replicate this table go back to the Trait Data and Analysis Form. Choose to sort correlations by POSITION and select RETURN = 500. Then scroll down the list to Chr 7 and review the subset of positional candidates that share expression with App. You should see a list similar to that shown above. Gtf3c1 is a good biological candidate and has a high covariation in expression with App.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>2. Caveat:<span style="mso-spacerun: yes"> </span>Of course, the gene or genes that control App expression may not be in this list. A protein coding difference might be the ultimate cause of variation in App transcript level and the expression covariation might be close to zero. Our list may also simply be missing the right transcript since the microarray is not truly comprehensive. Furthermore, even if the list contains the QTL gene, an expression difference may only have been expressed early in development or even in another tissue such as liver. While it is important to recognize these caveats, it is equally important to devise a rational way to rank candidates given existing data. Coexpression is one of several criteria used to evaluate positional candidates. We will see others in the next slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>3. We can also assess the likelihood that candidates contain functional polymorphism in promoters and enhancers that affect their expression simply by mapping the transcripts of all candidate genes to see if they Òmap backÓ to the location of gene itself. A transcript that maps to its own location is referred to as a cis QTL. We essentially ask: Which of the transcripts listed in the Correlation Table above (from Gtf3c1 to Zranb1) has variation in expression that maps to Chr 7 at about 120 Mb?<span style="mso-spacerun: yes"> </span>The logic of this search is that if a gene controls the level of its own expression it is also much more likely to generate other downstream effects. The Gtf3c1 transcript is a weak cis QTL with a local LRS maximum of about 7.0 (D alleles are high). That is just about sufficient to declare it to be a cis QTL. [No whole genome correction is required and a point-wise p-value of 0.05 is the appropriate test. A p-value of 0.05 is roughly equivalent to an LRS of 6.0 (LOD = 1.3).]</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009.htm new file mode 100755 index 00000000..16351b5b --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Physical maps are zoomable"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0009.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:-.53%;left:1.72%;width:101.05%;height:8.65%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;position:absolute;top:18.36%;left:.91%;width:97.9%; height:75.51%'><span style='font-family:Verdana;font-size:64%'>Physical maps are zoomable</span><span style='font-family:Verdana;font-size:73%;mso-special-format: lastCR;display:none'><i><br> </i></span></div> </div> <img border=0 src="slide0009_image078.png" style='position:absolute;top:8.83%; left:3.31%;width:89.93%;height:41.69%'><img border=0 src="slide0009_image079.png" style='position:absolute;top:44.52%;left:7.54%; width:42.91%;height:48.76%'><img border=0 src="slide0009_image080.png" style='position:absolute;top:94.52%;left:0%;width:97.08%;height:3.71%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>An even higher blow-up of part of the Chr 7 physical map of variation in App expression in brain.<span style="mso-spacerun: yes"> </span>The QTL region actually extends from about 119 to 129.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. As mentioned in the previous slide another important approach to ranking candidates is based on the number of sequence variants that distinguish the parental strains. If we were sure that the sequences of the gene, its promoter, and its enhancers were identical between the strains then we could discount--but not eliminate--that gene as a candidate. The Gtf3c1 candidate almost falls into this category: of 663 known SNPs in and around this gene, only four differ between C57BL/6J and DBA/2J. Gtf3c1 is essentially identical-by-descent in these strains and is a less likely candidate. In contrast, if the two alleles of the gene have dozens of functional variants in exons, promoters, enhancers, and splice sites, then it becomes a higher priority candidate.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Of course it only takes a single critical sequence variant to generate downstream effects. The argument above is really about the prior probabilities. Where would you place your bets given the information at hand?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2.<span style="mso-spacerun: yes"> </span>If you scroll down the INTERVAL ANALYST you will find that Ctbp2 is a particularly interesting candidate that contains lots of SNPs (n = 75 and a SNP density of 0.55 SNP/Kb). Ctbp2 is also closer to our QTL peak than was Gtf3c1. Not only does Ctbp2 contain lots of SNPs but it is also is associated with a powerful cis QTL with an LRS of 24.2 (divide by 4.61 to get the equivalent LOD score of 5.25).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3.<span style="mso-spacerun: yes"> </span>At this high magnification, individual genes are distinct. They are color coded by their density of SNPs. Bright orange represents those genes that have a high SNP density (C57BL/6J versus DBA/2J), black represents genes with low SNP density. Roll the cursor over a gene block and its name will pop up, along with information on exon number.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>4.<span style="mso-spacerun: yes"> </span>Beneath the physical map you will find an INTERVAL ANALYST table that lists information on known genes in the region on which you have zoomed the Physical Map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>5.<span style="mso-spacerun: yes"> </span>As always: error-checking is important. Some genes may be missing from the Interval Analyst (recent additions or errors of omission). In this case the Zranb1 gene that is located just proximal to Ctbp2 is not listed in the INTERVAL ANALYST. Double-check the interval using the Genome Browser links (blue and beige horizontal bars) at the top of the PHYSICAL MAP.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image022.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image022.png new file mode 100755 index 00000000..e03c35ed --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image022.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image078.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image078.png new file mode 100755 index 00000000..93d21c90 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image078.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image079.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image079.png new file mode 100755 index 00000000..fdc27d23 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image079.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image080.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image080.png new file mode 100755 index 00000000..d2cb5ee3 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image080.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_notes_pane.htm new file mode 100755 index 00000000..39c42e72 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>An even higher blow-up of part of the Chr 7 physical map of variation in App expression in brain.<span style="mso-spacerun: yes"> </span>The QTL region actually extends from about 119 to 129.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. As mentioned in the previous slide another important approach to ranking candidates is based on the number of sequence variants that distinguish the parental strains. If we were sure that the sequences of the gene, its promoter, and its enhancers were identical between the strains then we could discount--but not eliminate--that gene as a candidate. The Gtf3c1 candidate almost falls into this category: of 663 known SNPs in and around this gene, only four differ between C57BL/6J and DBA/2J. Gtf3c1 is essentially identical-by-descent in these strains and is a less likely candidate. In contrast, if the two alleles of the gene have dozens of functional variants in exons, promoters, enhancers, and splice sites, then it becomes a higher priority candidate.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Of course it only takes a single critical sequence variant to generate downstream effects. The argument above is really about the prior probabilities. Where would you place your bets given the information at hand?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2.<span style="mso-spacerun: yes"> </span>If you scroll down the INTERVAL ANALYST you will find that Ctbp2 is a particularly interesting candidate that contains lots of SNPs (n = 75 and a SNP density of 0.55 SNP/Kb). Ctbp2 is also closer to our QTL peak than was Gtf3c1. Not only does Ctbp2 contain lots of SNPs but it is also is associated with a powerful cis QTL with an LRS of 24.2 (divide by 4.61 to get the equivalent LOD score of 5.25).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>3.<span style="mso-spacerun: yes"> </span>At this high magnification, individual genes are distinct. They are color coded by their density of SNPs. Bright orange represents those genes that have a high SNP density (C57BL/6J versus DBA/2J), black represents genes with low SNP density. Roll the cursor over a gene block and its name will pop up, along with information on exon number.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>4.<span style="mso-spacerun: yes"> </span>Beneath the physical map you will find an INTERVAL ANALYST table that lists information on known genes in the region on which you have zoomed the Physical Map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>5.<span style="mso-spacerun: yes"> </span>As always: error-checking is important. Some genes may be missing from the Interval Analyst (recent additions or errors of omission). In this case the Zranb1 gene that is located just proximal to Ctbp2 is not listed in the INTERVAL ANALYST. Double-check the interval using the Genome Browser links (blue and beige horizontal bars) at the top of the PHYSICAL MAP.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010.htm new file mode 100755 index 00000000..91cf9f00 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Evaluating Ctbp2 as a candidate QTL for App"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0010.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:0%;left:1.72%;width:106.35%;height:7.24%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;position:absolute;top:12.19%;left:.87%;width:99.12%; height:90.24%'><span style='font-family:Verdana;font-size:64%'>Evaluating </span><span style='font-family:Verdana;font-size:64%'><i>Ctbp2</i></span><span style='font-family:Verdana;font-size:64%'> as a candidate QTL for </span><span style='font-family:Verdana;font-size:64%'><i>App</i></span><span style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display: none'><i><br> </i></span></div> </div> <img border=0 src="slide0010_image082.png" style='position:absolute;top:94.52%; left:3.31%;width:96.68%;height:4.24%'><img border=0 src="slide0010_image083.png" style='position:absolute;top:7.77%;left:3.31%;width:48.34%;height:40.28%'> <div class=O style='position:absolute;top:52.82%;left:55.23%;width:35.76%; height:37.98%'><span style='position:absolute;top:0%;left:0%;width:94.81%'><span style='font-size:233%;color:#E9EB5D'>This is</span><span style='font-size:233%; color:#E9EB5D'><i> the </i></span></span><span style='position:absolute; top:16.74%;left:0%;width:95.92%'><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2 </i></span><span style='font-size:233%;color:#E9EB5D'>cis QTL, </span></span><span style='position:absolute;top:33.48%;left:0%;width:98.14%'><span style='font-size:233%;color:#E9EB5D'>but is detected </span></span><span style='position:absolute;top:49.76%;left:0%;width:94.81%'><span style='font-size:233%;color:#E9EB5D'>only in the </span></span><span style='position:absolute;top:66.51%;left:0%;width:100.0%'><span style='font-size:233%;color:#E9EB5D'>Rosen striatum </span></span><span style='position:absolute;top:83.25%;left:0%;width:94.81%'><span style='font-size:233%;color:#E9EB5D'>data set.</span><span style='font-size: 233%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></div> <div class=O style='position:absolute;top:16.25%;left:56.02%;width:48.21%; height:12.72%'><span style='position:absolute;top:0%;left:0%;width:94.78%'><span style='font-size:233%;color:#E9EB5D'>This is</span><span style='font-size:233%; color:#E9EB5D'><i> the App QTL </i></span></span><span style='position:absolute; top:48.61%;left:0%;width:100.0%'><span style='font-size:233%;color:#E9EB5D'>in the INIA data set. </span><span style='font-size:233%;color:#E9EB5D;mso-special-format: lastCR;display:none'><i><br> </i></span></span></div> <img border=0 src="slide0010_image084.png" style='position:absolute;top:39.39%; left:3.31%;width:48.47%;height:53.35%'><img border=0 src="slide0010_image085.png" style='position:absolute;top:10.95%;left:35.36%; width:.39%;height:72.79%'><img border=0 src="slide0010_image086.png" style='position:absolute;top:10.95%;left:31.52%;width:.39%;height:72.79%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>This slide illustrates one reason why Ctbp2 should be considered a high priority positional candidate gene that may modulate the expression level of App.<span style="mso-spacerun: yes"> </span>Ctbp2 is a strong cis QTL in some brain regions (here the data are taken from the striatum).<span style="mso-spacerun: yes"> </span>If Ctbp2 contains variants that modulate its own expression then these expression differences may produce many downstream effects. Of course, we now want to know much more about the known biology of Ctbp2. What kind of gene is it? To begin to answer that question we can use a number of resources listed in the LINKS page.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Verdana size=3> The App QTL is bimodal. Perhaps there are actually two causal factors in this region--one close to 123 Mb and the other close to 127 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. The precision of QTL mapping depends on several factors, including the effect size and interactions among QTLs modulating a trait, the number of genetic individuals that are studied, and the distribution of recombinations in the study population.<span style="mso-spacerun: yes"> </span>In the case above, the QTL(s) are likely to be confined to the interval from 120 to 132 Mb. The bootstrap test (yellow bars shown in some of the previous slides) can be usual for estimating the consistency of QTL peaks.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image023.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image023.png new file mode 100755 index 00000000..1d32d035 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image023.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image024.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image024.png new file mode 100755 index 00000000..152e5045 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image024.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image082.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image082.png new file mode 100755 index 00000000..cf5f70f7 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image082.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image083.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image083.png new file mode 100755 index 00000000..a5886d21 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image083.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image084.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image084.png new file mode 100755 index 00000000..7eb77319 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image084.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image085.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image085.png new file mode 100755 index 00000000..99f4d04d --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image085.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image086.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image086.png new file mode 100755 index 00000000..ac87ce02 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image086.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_notes_pane.htm new file mode 100755 index 00000000..bdb257fb --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>This slide illustrates one reason why Ctbp2 should be considered a high priority positional candidate gene that may modulate the expression level of App.<span style="mso-spacerun: yes"> </span>Ctbp2 is a strong cis QTL in some brain regions (here the data are taken from the striatum).<span style="mso-spacerun: yes"> </span>If Ctbp2 contains variants that modulate its own expression then these expression differences may produce many downstream effects. Of course, we now want to know much more about the known biology of Ctbp2. What kind of gene is it? To begin to answer that question we can use a number of resources listed in the LINKS page.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Verdana size=2> The App QTL is bimodal. Perhaps there are actually two causal factors in this region--one close to 123 Mb and the other close to 127 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2. The precision of QTL mapping depends on several factors, including the effect size and interactions among QTLs modulating a trait, the number of genetic individuals that are studied, and the distribution of recombinations in the study population.<span style="mso-spacerun: yes"> </span>In the case above, the QTL(s) are likely to be confined to the interval from 120 to 132 Mb. The bootstrap test (yellow bars shown in some of the previous slides) can be usual for estimating the consistency of QTL peaks.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011.htm new file mode 100755 index 00000000..dd8304f8 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Evaluating Ctbp2 using other resources"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0011.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:0%;left:1.72%;width:101.05%;height:8.65%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;position:absolute;top:18.36%;left:.91%;width:97.9%; height:75.51%'><span style='font-family:Verdana;font-size:64%'>Evaluating </span><span style='font-family:Verdana;font-size:64%'><i>Ctbp2</i></span><span style='font-family:Verdana;font-size:64%'> using other resources</span><span style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display: none'><i><br> </i></span></div> </div> <img border=0 src="slide0011_image087.png" style='position:absolute;top:10.07%; left:1.72%;width:48.21%;height:53.35%'><img border=0 src="slide0011_image088.png" style='position:absolute;top:40.81%;left:19.2%; width:78.54%;height:54.77%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Ctbp2 should also be considered a high priority biological candidate gene responsible for modulating App expression levels. The C-terminal binding protein 2 is a transcriptional co-repressor also known as Ribeye.</font><font face=Times-Roman size=3> The gene produces two transcripts encoding distinct proteins. The short form is a transcriptional repressor that binds a Pro-X-Asp-Leu-Ser peptide motif and interacts with several transcription factors including EVI1, ZFPM1, and ZFHX1A (aka TCF8, deltaEF1). The longer isoform is a major component of specialized synapses in photoreceptors. Both proteins contain a NAD+ binding domain similar to NAD+-dependent 2-hydroxyacid dehydrogenases.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. To find out more about CTBP2 protein and the Ctbp2 gene, link to iHOP at http://www.pdg.cnb.uam.es/UniPub/iHOP/ and type in CTBP2</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Try Arrowsmith at http://arrowsmith.psych.uic.edu/cgi-test/arrowsmith_uic/pubsmith.cgi</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. Both APP and CTBP2 are involved in oxidoreducatase activity or Notch signaling. To establish this common gene ontology visit NCBI<span style="mso-spacerun: yes"> </span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene and enter each gene symbol.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. You can get interesting hints regarding Ctbp2 expression partners by examining the genetic correlations between Ctbp2 probe set 1422887_a_at and all other transcripts on the M430 Affymetrix array. Use the Striatum data set because we already know from previous work (the previous slide) that this gene is a cis QTL.<span style="mso-spacerun: yes"> </span>You should be able to show that Ctbp2 and Notch3 have antagonistic expression patterns in striatum. The negative genetic correlation with E2f4 is even stronger. The transcript also has a high positive genetic correlation with Rdh14. Of particular interest with respect to APP protein processing, Ctbp2 covaries positively with Bace2 (the transcript of the beta site APP-cleaving enzyme 2).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_image025.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_image025.png new file mode 100755 index 00000000..d29a333f --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_image025.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_image087.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_image087.png new file mode 100755 index 00000000..a6ca39ae --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_image087.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_image088.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_image088.png new file mode 100755 index 00000000..c17a41bc --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_image088.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_notes_pane.htm new file mode 100755 index 00000000..c287e06e --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Ctbp2 should also be considered a high priority biological candidate gene responsible for modulating App expression levels. The C-terminal binding protein 2 is a transcriptional co-repressor also known as Ribeye.</font><font face=Times-Roman size=2> The gene produces two transcripts encoding distinct proteins. The short form is a transcriptional repressor that binds a Pro-X-Asp-Leu-Ser peptide motif and interacts with several transcription factors including EVI1, ZFPM1, and ZFHX1A (aka TCF8, deltaEF1). The longer isoform is a major component of specialized synapses in photoreceptors. Both proteins contain a NAD+ binding domain similar to NAD+-dependent 2-hydroxyacid dehydrogenases.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>1. To find out more about CTBP2 protein and the Ctbp2 gene, link to iHOP at http://www.pdg.cnb.uam.es/UniPub/iHOP/ and type in CTBP2</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Try Arrowsmith at http://arrowsmith.psych.uic.edu/cgi-test/arrowsmith_uic/pubsmith.cgi</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2. Both APP and CTBP2 are involved in oxidoreducatase activity or Notch signaling. To establish this common gene ontology visit NCBI<span style="mso-spacerun: yes"> </span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene and enter each gene symbol.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>3. You can get interesting hints regarding Ctbp2 expression partners by examining the genetic correlations between Ctbp2 probe set 1422887_a_at and all other transcripts on the M430 Affymetrix array. Use the Striatum data set because we already know from previous work (the previous slide) that this gene is a cis QTL.<span style="mso-spacerun: yes"> </span>You should be able to show that Ctbp2 and Notch3 have antagonistic expression patterns in striatum. The negative genetic correlation with E2f4 is even stronger. The transcript also has a high positive genetic correlation with Rdh14. Of particular interest with respect to APP protein processing, Ctbp2 covaries positively with Bace2 (the transcript of the beta site APP-cleaving enzyme 2).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0012.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0012.htm new file mode 100755 index 00000000..852e722e --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0012.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0012.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:-.35%;left:3.31%;width:93.64%;height:14.48%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:292; mso-text-indent-alt:0;position:absolute;top:0%;left:1.13%;width:97.59%; height:51.21%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Summary of Part 2</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </div> <div style='position:absolute;top:15.01%;left:5.96%;width:101.19%;height:31.09%'> <div class=O1 style='mso-margin-left-alt:432'></div> <div class=O2 style='mso-margin-left-alt:720'></div> <div class=O3 style='mso-margin-left-alt:1008'></div> <div class=O4 style='mso-margin-left-alt:1296'></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:0%; left:0%;width:86.25%;height:14.2%'><span style='position:absolute;top:0%; left:2.88%;width:97.11%'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.96%;font-family:Arial'>1.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Covered the basics of QTL analysis and mapping.<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:14.2%; left:0%;width:86.25%;height:14.2%'><span style='position:absolute;top:0%; left:2.88%;width:97.11%'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.96%;font-family:Arial'>2.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Reviewed difference between genetic and physical maps.<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:28.4%; left:0%;width:100.0%;height:42.61%'><span style='position:absolute;top:0%; left:2.48%;width:97.51%'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.55%;font-family:Arial'>3.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Discussed interpreting features of QTL maps including the LRS function, </span></span><span style='position: absolute;top:33.33%;left:2.48%;width:91.23%'><span style='font-family:"Gill Sans"; font-size:167%;color:#E9EB5D;mso-color-index:3'>the additive effect function, the bootstrap bars, and the permutation </span></span><span style='position: absolute;top:68.0%;left:2.48%;width:83.76%'><span style='font-family:"Gill Sans"; font-size:167%;color:#E9EB5D;mso-color-index:3'>thresholds.<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:71.59%; left:0%;width:88.35%;height:14.2%'><span style='position:absolute;top:0%; left:2.81%;width:97.18%'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.89%;font-family:Arial'>4.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Illustrated techniques to generate a list of positional candidates.<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:85.79%; left:0%;width:86.25%;height:14.2%'><span style='position:absolute;top:0%; left:2.88%;width:97.11%'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.96%;font-family:Arial'>5.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Discussed some factors used to evaluate candidate genes.</span></span></div> </div> <div class=O style='position:absolute;top:58.65%;left:5.96%;width:106.22%; height:22.26%'><span style='position:absolute;top:0%;left:0%;width:84.53%'><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'>What does a QTL signify? A good QTL is a claim that a particular </span></span><span style='position:absolute;top:19.84%;left:0%;width:96.38%'><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'>chromosomal region contains a causal source of variation in the phenotype. </span></span><span style='position:absolute;top:39.68%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'>The importance of this hypothesis depends on the quality and relevance of the </span></span><span style='position:absolute;top:59.52%;left:0%;width:90.89%'><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'>phenotype and the statistical strength of the QTL. As usual, test and be </span></span><span style='position:absolute;top:79.36%;left:0%;width:84.53%'><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'>skeptical.</span></span></div> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0012_image026.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0012_image026.png new file mode 100755 index 00000000..a0675ffc --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0012_image026.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0012_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0012_notes_pane.htm new file mode 100755 index 00000000..895ab29b --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0012_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>By clicking on the CORRELATION of the Atcay transcript to the App transcript, you can generate a Correlation plot between these two transcripts. In this App and Atcay scatterplot, each point is a strain mean value. For example, BXD33 and BXD8 have low App and Atcay expressions. The two parental strains and the F1 are also included in this plot.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013.htm new file mode 100755 index 00000000..f8993810 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Test Questions"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0013.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:0%;left:1.72%;width:101.05%;height:8.65%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;position:absolute;top:18.36%;left:.91%;width:97.9%; height:75.51%'><span style='font-family:Verdana;font-size:64%'>Test Questions</span><span style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display: none'><i><br> </i></span></div> </div> <div class=O style='position:absolute;top:11.83%;left:4.37%;width:108.34%; height:6.53%'><span style='font-size:233%;color:#E9EB5D'>1. Evaluate candidates for the Chr 3 </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span style='font-size:233%;color:#E9EB5D'> QTL.</span><span style='font-size:233%; color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></div> <div class=O style='position:absolute;top:24.02%;left:4.9%;width:100.92%; height:12.72%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size:233%;color:#E9EB5D'>2. Do </span><span style='font-size:233%; color:#E9EB5D'><i>App</i></span><span style='font-size:233%;color:#E9EB5D'> and </span><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span style='font-size:233%;color:#E9EB5D'> expression share any </span></span><span style='position:absolute;top:50.0%;left:0%;width:93.43%'><span style='font-size:233%;color:#E9EB5D'>other QTLs beside that on Chr 7?</span><span style='font-size:233%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></div> <div class=O style='position:absolute;top:43.99%;left:4.9%;width:102.91%; height:19.08%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size:233%;color:#E9EB5D'>3. Can you exploit literature mining tools to </span></span><span style='position:absolute;top:33.33%;left:0%;width:98.45%'><span style='font-size:233%;color:#E9EB5D'>find a strong relationship between </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span style='font-size: 233%;color:#E9EB5D'> and </span></span><span style='position:absolute; top:65.74%;left:0%;width:91.63%'><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span style='font-size:233%;color:#E9EB5D'>? </span><span style='font-size:233%; color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></div> <div class=O style='position:absolute;top:69.08%;left:4.9%;width:110.19%; height:12.72%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size:233%;color:#E9EB5D'>4. Why might the cis QTL for </span><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span style='font-size: 233%;color:#E9EB5D'> expression </span></span><span style='position:absolute; top:50.0%;left:0%;width:89.66%'><span style='font-size:233%;color:#E9EB5D'>only be detected in the striatum data set?</span><span style='font-size:233%; color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></div> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013_image027.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013_image027.png new file mode 100755 index 00000000..ba473846 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013_image027.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013_notes_pane.htm new file mode 100755 index 00000000..190b8653 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>A group of traits from many different databases can be selected and brought together for joint analysis. In this case all of the content of the BXD SELECTIONS is from a single BRAIN database, the top 20 neighbors of the App transcript from the Correlation Results table. Eight of these neighbors plus App is shown in the slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Helvetica size=2>All of items in the BXD SELECTIONS were selected using the SELECT ALL button</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. The buttons at the top (and bottom) of this page can do some cool stuff. We will work with NETWORK GRAPH first.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>3. Think of the SELECTIONS as your shopping cart. You go to different aisles in the supermarket to acquire different types of items of interest. These could include transcripts, classical phenotypes (longevity, brain weight, prepulse inhibition, iron levels in midbrain). ÒChecking outÓ in this case involves doing some analysis with the items in the cart.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>4. Different tools handle different numbers of items. Most will handle up to 100 traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014.htm new file mode 100755 index 00000000..e5de4030 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Contact for comments and improvements:"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0014.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:2.29%;left:2.51%;width:94.43%;height:9.89%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-358 0 -1";position:absolute;top:19.64%; left:1.4%;width:97.47%;height:69.64%'><span style='font-size:73%'><i>Contact for comments and improvements:</i></span><span style='font-size:82%;mso-special-format: lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:16.6%;left:6.62%;width:90.19%;height:24.38%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-358 0 -1";position:absolute;top:0%; left:1.46%;width:97.35%;height:100.0%'><span style='position:absolute; top:0%;left:0%;width:100.0%'><span style='font-size:82%'>rwilliam@nb.utmem.edu<br> </span></span><span style='position:absolute;top:34.05%;left:4.67%;width:95.47%'><span style='font-size:82%'><br> </span></span><span style='position:absolute; top:68.11%;left:4.67%;width:95.47%'><span style='font-size:82%;mso-special-format: lastCR;display:none'><br> </span></span></div> </div> <div class=O style='position:absolute;top:27.56%;left:9.4%;width:50.59%; height:7.77%'><span style='font-family:"Gill Sans";font-size:300%;color:#E9EB5D'>kmanly@utmem.edu</span></div> <div class=O style='position:absolute;top:83.56%;left:4.37%;width:108.34%; height:15.9%'><span style='position:absolute;top:0%;left:0%;width:90.83%'><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D'>The </span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D'><i>App</i></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D'> findings reviewed in this presentation are part of an </span></span><span style='position:absolute; top:33.33%;left:0%;width:100.0%'><span style='font-family:"Gill Sans"; font-size:200%;color:#E9EB5D'>ongoing study by R. Williams. R. Homayouni, and R. Clark (July 15, </span></span><span style='position:absolute;top:66.66%; left:0%;width:84.35%'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'>2005)</span><span style='font-family:"Gill Sans";font-size:300%; color:#E9EB5D;mso-special-format:lastCR;display:none'><br> </span></span></div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>END</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image029.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image029.png new file mode 100755 index 00000000..8f560834 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image029.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image031.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image031.png new file mode 100755 index 00000000..8d72b4c1 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image031.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image033.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image033.png new file mode 100755 index 00000000..c1cd1c01 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image033.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_notes_pane.htm new file mode 100755 index 00000000..4a9d3b57 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>END</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015.htm new file mode 100755 index 00000000..89e5d8e5 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015.htm @@ -0,0 +1,155 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: The GeneNetwork and WebQTL : PART 2 link to www.genenetwork.org"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0015.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0.02 * g_width; myheight = 0.18 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.02 * g_height; myleft = 0 * g_width; myheight = 0.13 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-277 0 -1";mso-margin-left-alt:232; mso-text-indent-alt:0;mso-line-spacing:"-277 0 -1";mso-margin-left-alt:232; mso-text-indent-alt:0'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:73%'>The GeneNetwork and WebQTL : PART 2<span style="mso-spacerun: yes"> </span><br> </span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0.04 * g_width; myheight = 0.06 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:73%'>link to www.genenetwork.org</span><span style='font-size:73%;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </layer><script> + mytop = 0.24 * g_height; myleft = 0.05 * g_width; myheight = 0.68 * g_height; mywidth = 0.54 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.42 * g_height; mywidth = 0.52 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.21 * g_height; mywidth = 0.52 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.46 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part 1. How to study </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.41 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>expression variation </span></span></layer><script> + mytop = 0.1 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.47 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>and genetic correlation </span></span></layer><script> + mytop = 0.15 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.41 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>(slides 2–17)<br> </span></span></layer></div> </layer><script> + mytop = 0.25 * g_height; myleft = 0 * g_width; myheight = 0.16 * g_height; mywidth = 0.48 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.46 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part 2. Discovering </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.43 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>upstream modulators </span></span></layer><script> + mytop = 0.1 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.41 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>(slides 18–29)</span></span></layer></div> </layer></div> </layer></div> </layer><script> + mytop = 0.17 * g_height; myleft = 0.74 * g_width; myheight = 0.64 * g_height; mywidth = 0.23 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.74 * g_width; +yy = 0.17 * g_height; +ht = 0.64 * g_height; +wd = 0.23 * g_width; +document.write( +'<img border=0 src="slide0001_image001.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.75 * g_height; myleft = 0.74 * g_width; myheight = 0.14 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:"Arial Rounded MT Bold";font-size:233%;color:#6E6E6E'>RNA</span><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; display:none'><br> </span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.82 * g_height; myleft = 0.04 * g_width; myheight = 0.18 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div></div> </layer><script> + mytop = 0.5 * g_height; myleft = 0.48 * g_width; myheight = 0.13 * g_height; mywidth = 0.25 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.48 * g_width; +yy = 0.5 * g_height; +ht = 0.13 * g_height; +wd = 0.25 * g_width; +document.write( +'<img border=0 src="slide0001_image002.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Part 2: Discovering upstream modulators and quantitative trait loci (QTLs). A quantitative trait locus is a chromosomal region that harbors one or a few polymorphic gene loci that influence a trait. We are going to be looking for QTLs that modulate the steady state expression level of App in the adult mouse forebrain.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_image034.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_image034.png new file mode 100755 index 00000000..dafa2898 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_image034.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_image035.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_image035.png new file mode 100755 index 00000000..35566d47 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_image035.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_notes_pane.htm new file mode 100755 index 00000000..c4c4ec6d --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Going back to the Trait Data and Analysis Form window, we have computed the correlations between strain variation in App expression level and other classical phenotypes that have already been measured in many of the same BXD strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Helvetica size=2>The number of common strains varies widely--in this case from 14 to 23 strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. We can add these traits (four are selected) to our BXD SELECTIONS window.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016.htm new file mode 100755 index 00000000..ea69ff33 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016.htm @@ -0,0 +1,919 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0016.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; 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+//--> +</script></div> </layer><script> + mytop = 0.92 * g_height; myleft = 0.08 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.02 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-134 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Times;font-size:117%;color:white;display:none'><br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; 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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Times;font-size:117%; color:white;display:none'><br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.02 * g_height; mywidth = 0.29 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Times;font-size:117%; color:white;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.02 * g_height; myleft = -0.05 * g_width; myheight = 0.11 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-240 0 0";mso-margin-left-alt: 16;mso-text-indent-alt:16'><span style='font-family:Arial;font-size:267%; color:#E9EB5D'>How to make recombinant inbred strains (RI)</span><span style='font-family:Arial;font-size:150%;color:aqua;display:none'><br> </span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0.06 * g_width; myheight = 0.03 * g_height; mywidth = 0.92 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-160 0 0";mso-margin-left-alt: 16;mso-text-indent-alt:16'><span style='font-family:Arial;font-size:150%; color:aqua;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.28 * g_height; myleft = 0.45 * g_width; myheight = 0.01 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.45 * g_width; +yy = 0.28 * g_height; +ht = 0.01 * g_height; +wd = 0.18 * g_width; +document.write( +'<img border=0 src="slide0002_image003.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.28 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.28 * g_width; +yy = 0.2 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0002_image004.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0.25 * g_width; myheight = 0.09 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>C57BL/6J (B)<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.3 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.3 * g_width; +yy = 0.2 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0002_image005.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0.62 * g_width; myheight = 0.09 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>DBA/2J (D)<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.66 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.66 * g_width; +yy = 0.2 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0002_image006.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.23 * g_width; myheight = 0.01 * g_height; mywidth = 0.5 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.23 * g_width; +yy = 0.35 * g_height; +ht = 0.01 * g_height; +wd = 0.5 * g_width; +document.write( +'<img border=0 src="slide0002_image007.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.24 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.24 * g_width; +yy = 0.35 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0002_image008.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.4 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.4 * g_width; +yy = 0.35 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0002_image009.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.57 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.57 * g_width; +yy = 0.35 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0002_image010.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.74 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.74 * g_width; +yy = 0.35 * g_height; +ht = 0.03 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0002_image011.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.42 * g_height; myleft = 0.05 * g_width; myheight = 0.12 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F1<br> </b></span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format: lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.39 * g_height; myleft = 0.22 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.22 * g_width; +yy = 0.39 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0002_image012.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.39 * g_height; myleft = 0.38 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.38 * g_width; +yy = 0.39 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0002_image013.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.39 * g_height; myleft = 0.55 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.55 * g_width; +yy = 0.39 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0002_image014.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.39 * g_height; myleft = 0.72 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.72 * g_width; +yy = 0.39 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0002_image015.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.43 * g_height; myleft = 0.43 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.43 * g_width; +yy = 0.43 * g_height; +ht = 0.03 * g_height; +wd = 0.11 * g_width; +document.write( +'<img border=0 src="slide0002_image016.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.6 * g_height; myleft = 0.2 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.2 * g_width; +yy = 0.6 * g_height; +ht = 0.03 * g_height; +wd = 0.09 * g_width; +document.write( +'<img border=0 src="slide0002_image017.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.71 * g_height; myleft = 0.58 * g_width; myheight = 0.26 * g_height; mywidth = 0.2 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.03 * g_height; myleft = 0.01 * g_width; myheight = 0.22 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.15 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:117%; color:#FFFF99'><b>20 generations </b></span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:117%; color:#FFFF99'><b>brother-sister </b></span></span></layer><script> + mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:117%; color:#FFFF99'><b>matings</b></span><span style='font-family:Arial;font-size: 233%;color:#FFFF99;display:none'><b><br> </b></span></span></layer></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:233%; color:#FFFF99;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.6 * g_height; myleft = 0.5 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.5 * g_width; +yy = 0.6 * g_height; +ht = 0.03 * g_height; +wd = 0.09 * g_width; +document.write( +'<img border=0 src="slide0002_image018.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.62 * g_height; myleft = 0.54 * g_width; myheight = 0.28 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.54 * g_width; +yy = 0.62 * g_height; +ht = 0.28 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0002_image019.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.61 * g_height; myleft = 0.79 * g_width; myheight = 0.03 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.79 * g_width; +yy = 0.61 * g_height; +ht = 0.03 * g_height; +wd = 0.1 * g_width; +document.write( +'<img border=0 src="slide0002_image020.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.62 * g_height; myleft = 0.83 * g_width; myheight = 0.28 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.83 * g_width; +yy = 0.62 * g_height; +ht = 0.28 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0002_image021.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.92 * g_height; myleft = 0.21 * g_width; myheight = 0.09 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD1</span><span style='font-family:Arial;font-size:150%;color:#484848;display:none'><br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#484848;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.92 * g_height; myleft = 0.51 * g_width; myheight = 0.09 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD2<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.92 * g_height; myleft = 0.8 * g_width; myheight = 0.05 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:"-173 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;mso-line-spacing:"-173 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>BXD80</span></div> </layer></div> </layer><script> + mytop = 0.9 * g_height; myleft = 0.64 * g_width; myheight = 0.17 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.15 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-341 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:300%;color:#FFFF99'>+ É +<br> </span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-341 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:300%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.62 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F2<br> </b></span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format: lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.18 * g_width; myheight = 0.01 * g_height; mywidth = 0.75 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.18 * g_width; +yy = 0.54 * g_height; +ht = 0.01 * g_height; +wd = 0.75 * g_width; +document.write( +'<img border=0 src="slide0002_image022.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.17 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.17 * g_width; +yy = 0.54 * g_height; +ht = 0.03 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0002_image023.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.32 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.32 * g_width; +yy = 0.54 * g_height; +ht = 0.03 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0002_image024.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.48 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.48 * g_width; +yy = 0.54 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0002_image025.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.62 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.62 * g_width; +yy = 0.54 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0002_image026.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.77 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.77 * g_width; +yy = 0.54 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0002_image027.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.92 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.92 * g_width; +yy = 0.54 * g_height; +ht = 0.03 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0002_image028.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.44 * g_height; myleft = 0.49 * g_width; myheight = 0.1 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.49 * g_width; +yy = 0.44 * g_height; +ht = 0.1 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0002_image029.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.15 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.15 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0002_image030.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.3 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.3 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0002_image031.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.46 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.46 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0002_image032.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.6 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.6 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0002_image033.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.75 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.75 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0002_image034.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.9 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.9 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0002_image035.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.84 * g_height; myleft = 0.56 * g_width; myheight = 0.01 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.56 * g_width; +yy = 0.84 * g_height; +ht = 0.01 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0002_image036.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.8 * g_height; myleft = 0.25 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.25 * g_width; +yy = 0.8 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0002_image037.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.84 * g_height; myleft = 0.86 * g_width; myheight = 0.02 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.86 * g_width; +yy = 0.84 * g_height; +ht = 0.02 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0002_image038.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.75 * g_height; myleft = 0.01 * g_width; myheight = 0.13 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'><b>BXD RI<br> </b></span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'><b>Strain set<br> </b></span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.01 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.12 * g_height; myleft = 0.14 * g_width; myheight = 0.06 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.14 * g_width; +yy = 0.12 * g_height; +ht = 0.06 * g_height; +wd = 0.1 * g_width; +document.write( +'<img border=0 src="slide0002_image039.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.76 * g_width; myheight = 0.08 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.76 * g_width; +yy = 0.1 * g_height; +ht = 0.08 * g_height; +wd = 0.14 * g_width; +document.write( +'<img border=0 src="slide0002_image040.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.17 * g_width; myheight = 0.13 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>fully<br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>inbred<br> </span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.38 * g_height; myleft = 0.02 * g_width; myheight = 0.09 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>isogenic<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.01 * g_width; myheight = 0.13 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>hetero-<br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>geneous<br> </span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.74 * g_height; myleft = 0.29 * g_width; myheight = 0.21 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.19 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.15 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>Recombined </span></span></layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>chromosomes </span></span></layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>are needed for </span></span></layer><script> + mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>mapping<br> </span></span></layer></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.25 * g_width; myheight = 0.09 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>female<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.64 * g_width; myheight = 0.09 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>male<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.3 * g_height; myleft = 0.78 * g_width; myheight = 0.09 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:117%;color:#FFFF99'>chromosome pair</span><span style='font-family:Arial;font-size:150%;color:#FFFF99; display:none'><br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.31 * g_height; myleft = 0.65 * g_width; myheight = 0.02 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.65 * g_width; +yy = 0.31 * g_height; +ht = 0.02 * g_height; +wd = 0.12 * g_width; +document.write( +'<img border=0 src="slide0002_image041.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.86 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.12 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%; color:#E9EB5D'>Inbred<br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%; color:#E9EB5D'>Isogenic<br> </span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%; color:#E9EB5D'>siblings</span><span style='font-family:Arial;font-size:117%; color:aqua;display:none'><br> </span></div> </layer><script> + mytop = 0.09 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%; color:aqua;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.79 * g_height; myleft = 0.83 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.83 * g_width; +yy = 0.79 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0002_image042.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.84 * g_height; myleft = 0.83 * g_width; myheight = 0.02 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.83 * g_width; +yy = 0.84 * g_height; +ht = 0.02 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0002_image043.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.79 * g_height; myleft = 0.53 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.53 * g_width; +yy = 0.79 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0002_image044.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.83 * g_height; myleft = 0.53 * g_width; myheight = 0.01 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.53 * g_width; +yy = 0.83 * g_height; +ht = 0.01 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0002_image045.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.8 * g_height; myleft = 0.23 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.23 * g_width; +yy = 0.8 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0002_image046.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.18 * g_height; myleft = 0.43 * g_width; myheight = 0.09 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:"-341 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;mso-line-spacing:"-341 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Arial;font-size:300%; color:aqua'>B</span><span style='font-family:Arial;font-size:300%;color:#FFFF99'>X</span><span style='font-family:Arial;font-size:300%;color:#FF1911'>D</span></div> </layer></div> </layer><script> + mytop = 0.27 * g_height; myleft = 0.32 * g_width; myheight = 0.04 * g_height; mywidth = 0.31 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.32 * g_width; +yy = 0.27 * g_height; +ht = 0.04 * g_height; +wd = 0.31 * g_width; +document.write( +'<img border=0 src="slide0002_image047.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.66 * g_height; myleft = 0.6 * g_width; myheight = 0.03 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.6 * g_width; +yy = 0.66 * g_height; +ht = 0.03 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0002_image048.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.64 * g_height; myleft = 0.15 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.15 * g_width; +yy = 0.64 * g_height; +ht = 0.05 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0002_image049.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.75 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.75 * g_width; +yy = 0.57 * g_height; +ht = 0.05 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0002_image050.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.28 * g_height; myleft = 0.48 * g_width; myheight = 0.08 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.48 * g_width; +yy = 0.28 * g_height; +ht = 0.08 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0002_image051.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.62 * g_height; myleft = 0.23 * g_width; myheight = 0.16 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.23 * g_width; +yy = 0.62 * g_height; +ht = 0.16 * g_height; +wd = 0.03 * g_width; +document.write( +'<img border=0 src="slide0002_image052.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.61 * g_height; myleft = 0.63 * g_width; myheight = 0.08 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.63 * g_width; +yy = 0.61 * g_height; +ht = 0.08 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0002_image053.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The next few slides provide a short introduction to mapping the loci that are responsible for variation in a trait such as App expression level. These modulatory regions of the genome are sometimes called quantitative trait loci or QTLs. You may want to do some independent reading on this topic if this is your first exposure to QTL analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The genetic reference population (GRP) of BXD recombinant inbred strains were originally generated about 25 years ago by Benjamin Taylor at The Jackson Laboratory. He crossed female C57BL/6J mice with male DBA/2J mice to generate the F1 and F2 progeny. At the bottom of this slide we have schematized one chromosome pair from three of the BXD RI strains.<span style="mso-spacerun: yes"> </span>The dashed vertical lines that lead to the final BXD RI lines involve 21 full sib matings (about 7 years of breeding). Some lines die out during inbreeding. For example, there is no longer any BXD3 strain.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. Over the last decade, our group (Lu Lu and Rob Williams) and Jeremy Peirce and Lee Silver at Princeton have enlarged Ben TaylorÕs set. There are now just over 80 BXD strains. They have all been genotyped using about 13,700 markers (SNPs and microsatellites). These markers are used to define the ÒblueÓ and ÒredÓ regions of the chromosomes as shown in the figure above.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. Chromosomes of RI GRPs usually have about 4 times as many recombinations as those of F2 animals. However, unlike an F2, both chromosomes of an RI are identical. Therefore, 50 RI strains contain as many recombinations as 100 F2 animals.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. BXD43 through BXD100 were generated using a special method that resulted in a further doubling of the average recombination density per chromosome. The entire set of 80 BXDs therefore contains as many recombinations as about 260 F2 animals.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016_image036.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016_image036.png new file mode 100755 index 00000000..baa1d807 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016_image036.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016_notes_pane.htm new file mode 100755 index 00000000..f5776dad --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>We have computed the Network Graph, now using other types of traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Saline Hot Plate Latency is the green node labeled 10020.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Freezing (fear) is the green node labeled 10447.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0017.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0017.htm new file mode 100755 index 00000000..cc8ff93a --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0017.htm @@ -0,0 +1,421 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0017.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; 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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.4 * g_height; myleft = 0.73 * g_width; myheight = 0.05 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.73 * g_width; +yy = 0.4 * g_height; +ht = 0.05 * g_height; +wd = 0.14 * g_width; +document.write( +'<img border=0 src="slide0003_image054.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.4 * g_height; myleft = 0.74 * g_width; myheight = 0.07 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Gadget;font-size:150%;color:white'>aa<br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Gadget;font-size:150%;color:white;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0.73 * g_width; myheight = 0.05 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.73 * g_width; +yy = 0.16 * g_height; +ht = 0.05 * g_height; +wd = 0.14 * g_width; +document.write( +'<img border=0 src="slide0003_image055.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0.74 * g_width; myheight = 0.07 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Gadget;font-size:150%;color:white'>aaaa<br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Gadget;font-size:150%;color:white;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.71 * g_width; myheight = 0.19 * g_height; mywidth = 0.25 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.24 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.24 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:267%;color:#E2EBF0'>D2 strain</span><span style='font-family:Palatino;font-size:333%;color:#FBFDB8;display:none'><br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-family:Palatino;font-size:333%;color:#FBFDB8;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.43 * g_height; myleft = 0.71 * g_width; myheight = 0.19 * g_height; mywidth = 0.25 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.02 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.24 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.24 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:267%;color:#F6BF69'>B6 strain</span><span style='font-family:Palatino;font-size:333%;color:#F6BF69;display:none'><br> </span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-family:Palatino;font-size:333%;color:#F6BF69;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.17 * g_height; myleft = 0.31 * g_width; myheight = 0.42 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.31 * g_width; +yy = 0.17 * g_height; +ht = 0.42 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0003_image056.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.4 * g_height; myleft = 0.31 * g_width; myheight = 0.03 * g_height; mywidth = 0.39 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.31 * g_width; +yy = 0.4 * g_height; +ht = 0.03 * g_height; +wd = 0.39 * g_width; +document.write( +'<img border=0 src="slide0003_image057.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.38 * g_width; myheight = 0.26 * g_height; mywidth = 0.3 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.23 * g_height; mywidth = 0.27 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.13 * g_height; mywidth = 0.27 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-320 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.27 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'><i>amount of </i></span></span></layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.27 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'><i>transcript</i></span><span style='font-family:Palatino;font-size:367%;color:#E9EB5D;display:none'><br> </span></span></layer></div> </layer><script> + mytop = 0.14 * g_height; myleft = 0 * g_width; myheight = 0.09 * g_height; mywidth = 0.27 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-422 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-family:Palatino;font-size:367%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0.72 * g_width; myheight = 0.19 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:267%;color:white'>4 </span><span style='font-size: 233%;color:white'>units</span><span style='font-family:Palatino;font-size:333%; color:#E9EB5D;display:none'><br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-family:Palatino;font-size:333%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.29 * g_height; myleft = 0.72 * g_width; myheight = 0.19 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.02 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:267%;color:white'>2</span><span style='font-size: 233%;color:white'> units</span><span style='font-family:Palatino;font-size: 333%;color:#E9EB5D;display:none'><br> </span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-family:Palatino;font-size:333%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0.31 * g_width; myheight = 0.05 * g_height; mywidth = 0.4 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.31 * g_width; +yy = 0.15 * g_height; +ht = 0.05 * g_height; +wd = 0.4 * g_width; +document.write( +'<img border=0 src="slide0003_image058.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.17 * g_height; myleft = 0.09 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#E2EBF0'>D<br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.17 * g_height; myleft = 0.17 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69'>B<br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.79 * g_height; myleft = 0.05 * g_width; myheight = 0.13 * g_height; mywidth = 1.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.12 * g_height; mywidth = 1.02 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:"-256 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;mso-line-spacing:"-256 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.02 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E2EBF0'>D</span><span style='font-size:233%;color:#E9EB5D'> </span><span style='font-size:200%; color:#E9EB5D'>and </span><span style='font-size:233%;color:#F6BF69'>B</span><span style='font-size:233%;color:#E9EB5D'> </span><span style='font-size:200%; color:#E9EB5D'>may be SNP-like variants in the promoter </span></span></layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 1.02 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:200%;color:#E9EB5D'>itself (cis QTL) or in </span><span style='font-size:200%;color:#EAEC5E'>upstream genes (trans QTLs)</span><span style='font-size:300%;color:#E9EB5D'>.</span></span></layer></div> </layer></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.04 * g_width; myheight = 0.16 * g_height; mywidth = 0.22 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.22 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-233 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-size:200%;color:#E9EB5D'>UPSTREAM<br> </span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.22 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-233 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-size:200%;color:#E9EB5D'>modulators<br> </span></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.01 * g_width; myheight = 0.05 * g_height; mywidth = 0.2 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-233 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-size:200%;color:#E9EB5D; mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.44 * g_width; myheight = 0.17 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:300%;color:#E2EBF0'>High<br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.63 * g_height; myleft = 0.08 * g_width; myheight = 0.17 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#E2EBF0'>D<br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.63 * g_height; myleft = 0.15 * g_width; myheight = 0.17 * g_height; mywidth = 0.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69'>B<br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.71 * g_height; myleft = 0.07 * g_width; myheight = 0.12 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D'><i>cis QTL</i></span><span style='font-size:200%;color:#E9EB5D;display:none'><br> </span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.57 * g_height; myleft = -0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = -0.01 * g_width; +yy = 0.57 * g_height; +ht = 0.07 * g_height; +wd = 1.01 * g_width; +document.write( +'<img border=0 src="slide0003_image059.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.44 * g_height; myleft = 0.47 * g_width; myheight = 0.12 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-272 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:233%;color:#F6BF69'>Low<br> </span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-272 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:233%;color:#F6BF69;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.58 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.04 * g_height; mywidth = 1.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:"-200 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;mso-line-spacing:"-200 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Gadget;font-size:167%; color:white'>>>>>PROMOTER--ATG-Exon1-Intron1-Exon2-Intron2 - etc-3'UTR >>>>></span></div> </layer></div> </layer><script> + mytop = 0.37 * g_height; myleft = 0.08 * g_width; myheight = 0.2 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.08 * g_width; +yy = 0.37 * g_height; +ht = 0.2 * g_height; +wd = 0.13 * g_width; +document.write( +'<img border=0 src="slide0003_image060.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.4 * g_height; myleft = 0.1 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> + mytop = 0.4 * g_height; myleft = 0.18 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); 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mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;display:none'><b><br> </b></span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> + mytop = 0.27 * g_height; myleft = 0.04 * g_width; myheight = 0.21 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.04 * g_width; +yy = 0.27 * g_height; +ht = 0.21 * g_height; +wd = 0.21 * g_width; +document.write( +'<img border=0 src="slide0003_image062.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.27 * g_height; myleft = 0.05 * g_width; myheight = 0.12 * g_height; mywidth = 0.2 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D'><i>trans QTL</i></span><span style='font-size:200%;color:#E9EB5D;display:none'><br> </span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>This slide is illustrates two major types of QTLs that modulate variability in transcript-relative steady state abundance.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. cis QTLs are defined as QTLs that are closely linked to the gene whose transcript is the measured trait. For example, a polymorphism in the promoter that affects binding of a transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms in enhancers or may be in 3Õ UTR binding sites that affect message stability.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. trans QTLs map far enough away from the location of the gene that gives rise to the transcript that is being measured so that we can be fairly certain that the QTL is not in the gene itself. The most blatant type of trans QTL would be a polymorphism in a transcription factor. But in the majority of cases, the trans QTLs can be far removed in a mechanistic sense from the actual events modulating transcript abundance. That is why there are three overlapping arrows in the figure.<span style="mso-spacerun: yes"> </span>The way in which an upstream polymorphism influences a downstream difference in mRNA abundance can be indirect. Effects can:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>a.<span style="mso-spacerun: yes"> </span>cross tissue types (a polymorphic liver enzyme may affect CNS gene expression)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>b.<span style="mso-spacerun: yes"> </span>cross time (the modulator is only expressed for one day during development but has permanent effects in adults)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>c.<span style="mso-spacerun: yes"> </span>may be contingent on environmental factors (heat shock may trigger the expression of a polymorphic factor that affects mRNA abundance).</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018.htm new file mode 100755 index 00000000..a2c8a7db --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018.htm @@ -0,0 +1,115 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Discovering upstream modulatory loci"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0018.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; 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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.38 * g_height; myleft = 0.05 * g_width; myheight = 0.45 * g_height; mywidth = 0.84 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.05 * g_width; +yy = 0.38 * g_height; +ht = 0.45 * g_height; +wd = 0.84 * g_width; +document.write( +'<img border=0 src="slide0004_image063.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.08 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><span style='font-family:Verdana;font-size:64%'>Discovering upstream modulatory loci</span><span style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display: none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.18 * g_width; myheight = 0.25 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.18 * g_width; +yy = 0.2 * g_height; +ht = 0.25 * g_height; +wd = 0.19 * g_width; +document.write( +'<img border=0 src="slide0004_image064.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.32 * g_height; myleft = 0.78 * g_width; myheight = 0.25 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.78 * g_width; +yy = 0.32 * g_height; +ht = 0.25 * g_height; +wd = 0.19 * g_width; +document.write( +'<img border=0 src="slide0004_image065.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Please bring the Trait Data and Analysis window to the front and look for the Interval Mapping button. Confirm that you are back to the trait amyloid beta precursor protein.<span style="mso-spacerun: yes"> </span>If so, then just click the button.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notice that the default for:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Select Chrs (chromosomes) is ALL</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Select Mapping Scale is set to GENETIC</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Options: Permutation test YES<span style="mso-spacerun: yes"> </span>(2000 is the default number)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Options: Bootstrap test YES (2000 is the default number)</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_image037.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_image037.png new file mode 100755 index 00000000..a1cb20e4 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_image037.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_image038.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_image038.png new file mode 100755 index 00000000..e06bd0db --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_image038.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_notes_pane.htm new file mode 100755 index 00000000..9e0445f3 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Part 2: Discovering upstream modulators and quantitative trait loci (QTLs). A quantitative trait locus is a chromosomal region that harbors one or a few polymorphic gene loci that influence a trait. We are going to be looking for QTLs that modulate the steady state expression level of App in the adult mouse forebrain.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019.htm new file mode 100755 index 00000000..43fc12fd --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019.htm @@ -0,0 +1,155 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: WebQTL searches for upstream controllers"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0019.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; 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+</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'><i>WebQTL searches for upstream controllers</i></span><span style='font-family:Verdana; font-size:73%;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.71 * g_height; myleft = 0.34 * g_width; myheight = 0.19 * g_height; mywidth = 0.45 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.18 * g_height; mywidth = 0.44 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.44 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>App maps on Chr 16 (blue </i></span></span></layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.44 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>arrow points to the orange </i></span></span></layer><script> + mytop = 0.09 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.38 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>triangle) but the best </i></span></span></layer><script> + mytop = 0.13 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.38 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>locus is on Chr 7.</i></span><span style='font-size:233%;color:#E9EB5D;mso-special-format: lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0.01 * g_width; myheight = 0.53 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.08 * g_height; +ht = 0.53 * g_height; +wd = 0.98 * g_width; +document.write( +'<img border=0 src="slide0005_image066.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.46 * g_height; myleft = 0.15 * g_width; myheight = 0.53 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.15 * g_width; +yy = 0.46 * g_height; +ht = 0.53 * g_height; +wd = 0.15 * g_width; +document.write( +'<img border=0 src="slide0005_image067.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.46 * g_height; myleft = 0.8 * g_width; myheight = 0.53 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.8 * g_width; +yy = 0.46 * g_height; +ht = 0.53 * g_height; +wd = 0.1 * g_width; +document.write( +'<img border=0 src="slide0005_image068.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.41 * g_height; myleft = 0.76 * g_width; myheight = 0.22 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.76 * g_width; +yy = 0.41 * g_height; +ht = 0.22 * g_height; +wd = 0.11 * g_width; +document.write( +'<img border=0 src="slide0005_image069.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.41 * g_height; myleft = 0.29 * g_width; myheight = 0.24 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.29 * g_width; +yy = 0.41 * g_height; +ht = 0.24 * g_height; +wd = 0.12 * g_width; +document.write( +'<img border=0 src="slide0005_image070.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>This is a major output type: a so-called full-genome interval map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The X-axis represents all 19 autosomes and the X chromosome as if they were laid end to end with short gaps between the telomere of one chromosome and the centromere of the next chromosome (mouse chromosomes only have a single long arm and the centromere represents the origin of each chromosome for numerical purpose: 0 centimorgans at almost 0 megabases). The blue labels along the bottom of the figure list a subset of the 3795 markers that were used in mapping.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The thick blue wavy line running across chromosomes summarizes the strength of association between variation in the phenotype (App expression differences) and the two genotypes of all markers and the intervals between markers (hence, interval mapping).<span style="mso-spacerun: yes"> </span>The height of the wave (blue Y-axis to the left) provides the likelihood ratio statistic (LRS). Divide by 4.61 to convert these values to LOD scores.<span style="mso-spacerun: yes"> </span>Or you can read them as a chi-square-like statistic.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The red line and the red axis to the far right provide an estimate of the effect that a QTL has on expression of App (this estimate of the so-called additive effect tends to be too high). If the red line is below the X-axis then this means that the allele inherited from C57BL/6J (B6 or B) at a particular marker is associated with higher values. If the red line is above the X-axis then the DBA/2J allele (D2 or D) is associated with higher trait values. Multiply the additive effect size by 2 to estimate the difference between the set of strains that have the B/B genotype and those that have the D/D genotype at a specific marker. For example, on distal Chr 7 the red line peaks at a value of about 0.2. That means that this region of chromosome 2 is responsible for a 0.4 unit expression difference between B/B strains and the D/D strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The yellow histogram bars: These summarize the results of a whole-genome bootstrap of the trait that is performed 1000 times. What is a bootstrap? A bootstrap provides a method to evaluate whether results are robust. If we drop out one strain, do we still get the same results? When mapping quantitative traits, each strain normally gets one equally weighted vote. But using the bootstrap procedure, we give each strain a random weighting factor of between 0 and 1.<span style="mso-spacerun: yes"> </span>We then remap the trait and find THE SINGLE BEST LRS VALUE per bootstrap. We do this 1000 times. In this example, most bootstrap results cluster on Chr 3 and Chr 7 under the LRS peaks. That is somewhat reassuring. But notice that a substantial number of bootstrap are scattered around on other chromosomes. About 30% of the bootstrap resamples have a peak on Chr 7. That is pretty good, but does makes us realize that the sample we are working with is still quite small and fragile.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The horizontal dashed lines at 10.5 and 17.3 are the likelihood ratio statistic (LRS) values associated with the suggestive and significant genome-wide probabilities that were established by permutations of phenotypes across genotypes. We shuffle randomly 2000 times and obtain a distribution of peak LRS scores to generate a null distribution. Five percent of the time, one of these permuted data sets will have a peak LRS higher than 17.3. We call that level the 0.05 significance threshold for a whole genome scan. The p = 0.67 point is the suggestive level, and corresponds to the green dashed line.<span style="mso-spacerun: yes"> </span>These thresholds are conservative for transcripts that have expression variation that is highly heritable. The putative or suggestive QTL on Chr 3 is probably more than just suggestive.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>One other point: the mapping procedure we use is computationally very fast, but it is relatively simple. We are not looking for gene-gene interactions and we are not fitting multiple QTLs in combinations. Consider this QTL analysis a first pass that will highlight hot spots and warm spots that are worth following up on using more sophisticated models.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>CLICKABLE REGIONS:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. If you click on the Chromosome number then you will generate a new map just for that chromosome.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. If you click on the body of the map, say on the blue line, then you will generate a view on a 10 Mb window of that part of the genome from the UCSC Genome Browser web site.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. If you click on a marker symbol, then you will generate a new Trait data and Analysis window with the genotypes loaded into the window just like any other trait. More on this in Section 3.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>4. You can drag these maps off of the browser window and onto your desktop. They will be saved as PNG or PDF files. You can import them into Photoshop or other programs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>5. There is also an option at the bottom of the page to download a 2X higher resolution image of this plot for papers and presentations.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>6. You can also download the results of the analysis in a text format</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019_image039.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019_image039.png new file mode 100755 index 00000000..6cb8411f --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019_image039.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019_image040.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019_image040.png new file mode 100755 index 00000000..64ff0127 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019_image040.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019_image041.png 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differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019_notes_pane.htm new file mode 100755 index 00000000..67653ac4 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The next few slides provide a short introduction to mapping the loci that are responsible for variation in a trait such as App expression level. These modulatory regions of the genome are sometimes called quantitative trait loci or QTLs. You may want to do some independent reading on this topic if this is your first exposure to QTL analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The genetic reference population (GRP) of BXD recombinant inbred strains were originally generated about 25 years ago by Benjamin Taylor at The Jackson Laboratory. He crossed female C57BL/6J mice with male DBA/2J mice to generate the F1 and F2 progeny. At the bottom of this slide we have schematized one chromosome pair from three of the BXD RI strains.<span style="mso-spacerun: yes"> </span>The dashed vertical lines that lead to the final BXD RI lines involve 21 full sib matings (about 7 years of breeding). Some lines die out during inbreeding. For example, there is no longer any BXD3 strain.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>1. Over the last decade, our group (Lu Lu and Rob Williams) and Jeremy Peirce and Lee Silver at Princeton have enlarged Ben TaylorÕs set. There are now just over 80 BXD strains. They have all been genotyped using about 13,700 markers (SNPs and microsatellites). These markers are used to define the ÒblueÓ and ÒredÓ regions of the chromosomes as shown in the figure above.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2. Chromosomes of RI GRPs usually have about 4 times as many recombinations as those of F2 animals. However, unlike an F2, both chromosomes of an RI are identical. Therefore, 50 RI strains contain as many recombinations as 100 F2 animals.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>3. BXD43 through BXD100 were generated using a special method that resulted in a further doubling of the average recombination density per chromosome. The entire set of 80 BXDs therefore contains as many recombinations as about 260 F2 animals.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020.htm new file mode 100755 index 00000000..d148b0c8 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020.htm @@ -0,0 +1,113 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Genetic versus Physical maps for App expression"> <style media=print> <!--.sld {left:0px !important; 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mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'><i>Genetic versus Physical maps for App expression</i></span><span style='font-family: Verdana;font-size:73%;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0.01 * g_width; myheight = 0.39 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.08 * g_height; +ht = 0.39 * g_height; +wd = 0.98 * g_width; +document.write( +'<img border=0 src="slide0006_image071.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.01 * g_width; myheight = 0.54 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.35 * g_height; +ht = 0.54 * g_height; +wd = 0.98 * g_width; +document.write( +'<img border=0 src="slide0006_image072.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.91 * g_height; myleft = 0.05 * g_width; myheight = 0.07 * g_height; mywidth = 0.95 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.95 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:117%;color:#E9EB5D'><i>The difference between genetic and physical scale is analogous to measuring the </i></span></span></layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.92 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:117%;color:#E9EB5D'><i>separation between New York and Boston in either travel hours or kilometers</i></span><span style='font-size:150%;color:#E9EB5D'><i>.</i></span><span style='font-size: 167%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The map on the top has an X-axis scale based on frequency of recombinations events between markers (B to D transitions, see slide 19 for a color-coded example). These so-called genetic maps are scaled in centimorgan (recombinations per 100 gametes). In contrast, the physical map shown below the genetic map has an X-axis scale based on DNA length measured in nucleotides or base-pairs. Notice the large difference between the two maps in the size of Chr 19 (large on the genetic scale but small on the physical scale).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Also notice the large difference in the width of the chromosome 7 QTL peak. In mice, recombinations occur with higher frequency toward the telomeric side (right side) of each chromosome. As a result, genetic maps are stretched out more toward the telomere relative to a physical map. The QTL on distal Chr 7 is therefore actually more precisely mapped than might appear looking at the genetic map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The physical scale is becoming more useful than the genetic scale primarily because many other data types can be easily superimposed on a physical map. You will see more examples in the next several slides.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image090.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image090.png new file mode 100755 index 00000000..3f7c7606 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image090.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image091.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image091.png new file mode 100755 index 00000000..3f7c7606 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image091.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image092.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image092.png new file mode 100755 index 00000000..272f8318 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image092.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image093.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image093.png new file mode 100755 index 00000000..a526d207 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image093.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image094.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image094.png new file mode 100755 index 00000000..7a08eae6 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image094.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image095.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image095.png new file mode 100755 index 00000000..f2e33d2d --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image095.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image096.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image096.png new file mode 100755 index 00000000..2c8ab141 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image096.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image097.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image097.png new file mode 100755 index 00000000..9665dc0f --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image097.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image098.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image098.png new file mode 100755 index 00000000..4c8023d2 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image098.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_notes_pane.htm new file mode 100755 index 00000000..68c0fb55 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>This slide is illustrates two major types of QTLs that modulate variability in transcript-relative steady state abundance.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>1. cis QTLs are defined as QTLs that are closely linked to the gene whose transcript is the measured trait. For example, a polymorphism in the promoter that affects binding of a transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms in enhancers or may be in 3Õ UTR binding sites that affect message stability.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. trans QTLs map far enough away from the location of the gene that gives rise to the transcript that is being measured so that we can be fairly certain that the QTL is not in the gene itself. The most blatant type of trans QTL would be a polymorphism in a transcription factor. But in the majority of cases, the trans QTLs can be far removed in a mechanistic sense from the actual events modulating transcript abundance. That is why there are three overlapping arrows in the figure.<span style="mso-spacerun: yes"> </span>The way in which an upstream polymorphism influences a downstream difference in mRNA abundance can be indirect. Effects can:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2><span style="mso-spacerun: yes"> </span>a.<span style="mso-spacerun: yes"> </span>cross tissue types (a polymorphic liver enzyme may affect CNS gene expression)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2><span style="mso-spacerun: yes"> </span>b.<span style="mso-spacerun: yes"> </span>cross time (the modulator is only expressed for one day during development but has permanent effects in adults)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2><span style="mso-spacerun: yes"> </span>c.<span style="mso-spacerun: yes"> </span>may be contingent on environmental factors (heat shock may trigger the expression of a polymorphic factor that affects mRNA abundance).</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021.htm new file mode 100755 index 00000000..c7854145 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021.htm @@ -0,0 +1,110 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Physical map for distal chromosome 7"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0021.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Physical map for distal chromosome 7</span><span style='font-family:Verdana;font-size: 73%;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.04 * g_height; mywidth = 0.92 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-size:167%;color:#E9EB5D'>Distal Chr 7 from ~120 and 132 Mb may modulate</span><span style='font-size:167%;color:#E9EB5D'><i> App</i></span><span style='font-size:200%;color:#E9EB5D;mso-special-format: lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.93 * g_height; myleft = 0.06 * g_width; myheight = 0.03 * g_height; mywidth = 0.75 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.06 * g_width; +yy = 0.93 * g_height; +ht = 0.03 * g_height; +wd = 0.75 * g_width; +document.write( +'<img border=0 src="slide0007_image073.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0.06 * g_width; myheight = 0.75 * g_height; mywidth = 0.68 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.06 * g_width; +yy = 0.15 * g_height; +ht = 0.75 * g_height; +wd = 0.68 * g_width; +document.write( +'<img border=0 src="slide0007_image075.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Physical map of variation in App expression in brain on distal Chr 7 (a blow up of the whole-genome map on the previous slide).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Verdana size=3> You can now see that the X-axis is on a physical scale of megabases (Mb). The QTL peak is roughly between 120 and 132 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. The small irregular colored blocks and marks toward the top of the map mark the locations of genes superimposed on the physical map. Neighboring genes are offset slightly in the vertical axis for display purpose. Note one region of very high gene density from about 120 to 123 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. The orange hash marks along the X-axis represent the number of single nucleotide polymorphisms that distinguish the two parental strains (C57BL/6J and DBA/2J) from each other. We call this the SNP seismograph track (see Glossary for more details). Regions with low numbers of SNPs have closely matched sequences and are less likely to contain QTLs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>4. As before, the thin red line shows the additive effect size. By convention the positive values signify the D alleles are associated with higher expression of App in this region of Chr 7 than the B alleles. The maximum effect size is about +0.20 log2 expression units per D allele. The differences been the BB and DD genotypes (BB and DD because each strain has two alleles; one per chromosome) is therefore about 2^0.4 = 1.32 or a 32% increment in DD relative to BB at this locus.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>5. If you scroll just under the Physical Map you will see text that reads ÒDISPLAY from XXX Mb TO YYY MbÉ..Ó<span style="mso-spacerun: yes"> </span>These physical maps are zoomable, a feature we will exploit to evaluate candidate genes in this QTL interval.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image099.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image099.png new file mode 100755 index 00000000..891bc06c --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image099.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image100.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image100.png new file mode 100755 index 00000000..8905caa6 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image100.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image101.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image101.png new file mode 100755 index 00000000..7f5a5295 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image101.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_notes_pane.htm new file mode 100755 index 00000000..b1988954 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Please bring the Trait Data and Analysis window to the front and look for the Interval Mapping button. Confirm that you are back to the trait amyloid beta precursor protein.<span style="mso-spacerun: yes"> </span>If so, then just click the button.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Notice that the default for:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Select Chrs (chromosomes) is ALL</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Select Mapping Scale is set to GENETIC</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Options: Permutation test YES<span style="mso-spacerun: yes"> </span>(2000 is the default number)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Options: Bootstrap test YES (2000 is the default number)</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022.htm new file mode 100755 index 00000000..25d9a02e --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022.htm @@ -0,0 +1,134 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Evaluating candidate genes"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0022.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; 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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.34 * g_height; myleft = 0.01 * g_width; myheight = 0.61 * g_height; mywidth = 0.97 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.34 * g_height; +ht = 0.61 * g_height; +wd = 0.97 * g_width; +document.write( +'<img border=0 src="slide0008_image076.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = -0.01 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><span style='font-family:Verdana;font-size:64%'>Evaluating candidate genes</span><span style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display: none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0.01 * g_width; myheight = 0.22 * g_height; mywidth = 0.34 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.08 * g_height; +ht = 0.22 * g_height; +wd = 0.34 * g_width; +document.write( +'<img border=0 src="slide0008_image077.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0.69 * g_width; myheight = 0.17 * g_height; mywidth = 0.33 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.16 * g_height; mywidth = 0.31 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.31 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>Right position<br> </i></span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 0.31 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.31 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>and high </i></span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.31 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>correlation</i></span></span></layer></div> </layer></div> </layer></div> </layer><script> + mytop = 0.17 * g_height; myleft = 0.75 * g_width; myheight = 0.14 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.12 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center'><span style='font-size:267%;color:#E9EB5D'><i><span style="mso-spacerun: yes"> </span></i></span><span style='font-size:200%; color:#E9EB5D'><i>= better<br> </i></span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>candidates</i></span></div> </layer></div> </layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4><b>Evaluating candidate genes (CHECKED BOXES) responsible for variability in APP expression:</b></font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>A large number of genes are usually in the QTL interval and are therefore POSITIONAL CANDIDATES, but they will differ greatly in their biological and bioinformatic plausibility. Assume that the QTL has been located between 119 and 131 Mb (12 Mb). There will typically be 12 to 15 genes per Mb, so we might need to evaluate several hundred positional candidates. In this particular case there are about 100 known genes in this interval. Eight of these are highlighted in the table above with check marks in the boxes to the left.<span style="mso-spacerun: yes"> </span>We need to highlight and objectively score the biologically relevant subset of all 100 positional candidate genes. We could look through gene ontologies and expression levels to help us shorten the list. An alternate way available using WebQTL is to generate a list of those genes in this interval that have transcripts that co-vary in expression with App expression. That is what the table shows.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. To replicate this table go back to the Trait Data and Analysis Form. Choose to sort correlations by POSITION and select RETURN = 500. Then scroll down the list to Chr 7 and review the subset of positional candidates that share expression with App. You should see a list similar to that shown above. Gtf3c1 is a good biological candidate and has a high covariation in expression with App.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>2. Caveat:<span style="mso-spacerun: yes"> </span>Of course, the gene or genes that control App expression may not be in this list. A protein coding difference might be the ultimate cause of variation in App transcript level and the expression covariation might be close to zero. Our list may also simply be missing the right transcript since the microarray is not truly comprehensive. Furthermore, even if the list contains the QTL gene, an expression difference may only have been expressed early in development or even in another tissue such as liver. While it is important to recognize these caveats, it is equally important to devise a rational way to rank candidates given existing data. Coexpression is one of several criteria used to evaluate positional candidates. We will see others in the next slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>3. We can also assess the likelihood that candidates contain functional polymorphism in promoters and enhancers that affect their expression simply by mapping the transcripts of all candidate genes to see if they Òmap backÓ to the location of gene itself. A transcript that maps to its own location is referred to as a cis QTL. We essentially ask: Which of the transcripts listed in the Correlation Table above (from Gtf3c1 to Zranb1) has variation in expression that maps to Chr 7 at about 120 Mb?<span style="mso-spacerun: yes"> </span>The logic of this search is that if a gene controls the level of its own expression it is also much more likely to generate other downstream effects. The Gtf3c1 transcript is a weak cis QTL with a local LRS maximum of about 7.0 (D alleles are high). That is just about sufficient to declare it to be a cis QTL. [No whole genome correction is required and a point-wise p-value of 0.05 is the appropriate test. A p-value of 0.05 is roughly equivalent to an LRS of 6.0 (LOD = 1.3).]</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image102.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image102.png new file mode 100755 index 00000000..5ab7794c --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image102.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image103.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image103.png new file mode 100755 index 00000000..c26d4792 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image103.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image104.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image104.png new file mode 100755 index 00000000..af0745a5 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image104.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image105.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image105.png new file mode 100755 index 00000000..6ec88720 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image105.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image106.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image106.png new file mode 100755 index 00000000..9c156ddc --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image106.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_notes_pane.htm new file mode 100755 index 00000000..4d30f6e3 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>This is a major output type: a so-called full-genome interval map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The X-axis represents all 19 autosomes and the X chromosome as if they were laid end to end with short gaps between the telomere of one chromosome and the centromere of the next chromosome (mouse chromosomes only have a single long arm and the centromere represents the origin of each chromosome for numerical purpose: 0 centimorgans at almost 0 megabases). The blue labels along the bottom of the figure list a subset of the 3795 markers that were used in mapping.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The thick blue wavy line running across chromosomes summarizes the strength of association between variation in the phenotype (App expression differences) and the two genotypes of all markers and the intervals between markers (hence, interval mapping).<span style="mso-spacerun: yes"> </span>The height of the wave (blue Y-axis to the left) provides the likelihood ratio statistic (LRS). Divide by 4.61 to convert these values to LOD scores.<span style="mso-spacerun: yes"> </span>Or you can read them as a chi-square-like statistic.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The red line and the red axis to the far right provides an estimate of the effect that a QTL has on expression of App (this estimate of the so-called additive effect tends to be too high). If the red line is below the X-axis then this means that the allele inherited from C57BL/6J (B6 or B) at a particular marker is associated with higher values. If the red line is above the X-axis then the DBA/2J allele (D2 or D) is associated with higher trait values. Multiply the additive effect size by 2 to estimate the difference between the set of strains that have the B/B genotype and those that have the D/D genotype at a specific marker. For example, on distal Chr 7 the red line peaks at a value of about 0.2. That means that this region of chromosome 2 is responsible for a 0.4 unit expression difference between B/B strains and the D/D strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The yellow histogram bars: These summarize the results of a whole-genome bootstrap of the trait that is performed 1000 times. What is a bootstrap? A bootstrap provides a method to evaluate whether results are robust. If we drop out one strain, do we still get the same results? When mapping quantitative traits, each strain normally gets one equally weighted vote. But using the bootstrap procedure, we give each strain a random weighting factor of between 0 and 1.<span style="mso-spacerun: yes"> </span>We then remap the trait and find THE SINGLE BEST LRS VALUE per bootstrap. We do this 1000 times. In this example, most bootstrap results cluster on Chr 3 and Chr 7 under the LRS peaks. That is somewhat reassuring. But notice that a substantial number of bootstrap are scattered around on other chromosomes. About 30% of the bootstrap resamples have a peak on Chr 7. That is pretty good, but does makes us realize that the sample we are working with is still quite small and fragile.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The horizontal dashed lines at 10.5 and 17.3 are the likelihood ratio statistic (LRS) values associated with the suggestive and significant genome-wide probabilities that were established by permutations of phenotypes across genotypes. We shuffle randomly 2000 times and obtain a distribution of peak LRS scores to generate a null distribution. Five percent of the time, one of these permuted data sets will have a peak LRS higher than 17.3. We call that level the 0.05 significance threshold for a whole genome scan. The p = 0.67 point is the the suggestive level, and corresponds to the green dashed line.<span style="mso-spacerun: yes"> </span>These thresholds are conservative for transcripts that have expression variation that is highly heritable. The putative or suggestive QTL on Chr 3 is probably more than just suggestive.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>One other point: the mapping procedure we use is computationally very fast, but it is relatively simple. We are not looking for gene-gene interactions and we are not fitting multiple QTLs in combinations. Consider this QTL analysis a first pass that will highlight hot spots and warm spots that are worth following up on using more sophisticated models.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>CLICKABLE REGIONS:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>1. If you click on the Chromosome number then you will generate a new map just for that chromosome.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2. If you click on the body of the map, say on the blue line, then you will generate a view on a 10 Mb window of that part of the genome from the UCSC Genome Browser web site.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>3. If you click on a marker symbol, then you will generate a new Trait data and Analysis window with the genotypes loaded into the window just like any other trait. More on this in Section 3.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>4. You can drag these maps off of the browser window and onto your desktop. They will be saved as PNG or PDF files. You can import them into Photoshop or other programs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>5. There is also an option at the bottom of the page to download a 2X higher resolution image of this plot for papers and presentations.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>6. You can also download the results of the analysis in a text format</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023.htm new file mode 100755 index 00000000..fabf25c5 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023.htm @@ -0,0 +1,115 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Physical maps are zoomable"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; 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+</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Physical maps are zoomable</span><span style='font-family:Verdana;font-size:73%; mso-special-format:lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0.03 * g_width; myheight = 0.41 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.03 * g_width; +yy = 0.08 * g_height; +ht = 0.41 * g_height; +wd = 0.89 * g_width; +document.write( +'<img border=0 src="slide0009_image078.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.44 * g_height; myleft = 0.07 * g_width; myheight = 0.48 * g_height; mywidth = 0.42 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.07 * g_width; +yy = 0.44 * g_height; +ht = 0.48 * g_height; +wd = 0.42 * g_width; +document.write( +'<img border=0 src="slide0009_image079.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.94 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.97 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0 * g_width; +yy = 0.94 * g_height; +ht = 0.03 * g_height; +wd = 0.97 * g_width; +document.write( +'<img border=0 src="slide0009_image080.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>An even higher blow-up of part of the Chr 7 physical map of variation in App expression in brain.<span style="mso-spacerun: yes"> </span>The QTL region actually extends from about 119 to 129.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. As mentioned in the previous slide another important approach to ranking candidates is based on the number of sequence variants that distinguish the parental strains. If we were sure that the sequences of the gene, its promoter, and its enhancers were identical between the strains then we could discount--but not eliminate--that gene as a candidate. The Gtf3c1 candidate almost falls into this category: of 663 known SNPs in and around this gene, only four differ between C57BL/6J and DBA/2J. Gtf3c1 is essentially identical-by-descent in these strains and is a less likely candidate. In contrast, if the two alleles of the gene have dozens of functional variants in exons, promoters, enhancers, and splice sites, then it becomes a higher priority candidate.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Of course it only takes a single critical sequence variant to generate downstream effects. The argument above is really about the prior probabilities. Where would you place your bets given the information at hand?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2.<span style="mso-spacerun: yes"> </span>If you scroll down the INTERVAL ANALYST you will find that Ctbp2 is a particularly interesting candidate that contains lots of SNPs (n = 75 and a SNP density of 0.55 SNP/Kb). Ctbp2 is also closer to our QTL peak than was Gtf3c1. Not only does Ctbp2 contain lots of SNPs but it is also is associated with a powerful cis QTL with an LRS of 24.2 (divide by 4.61 to get the equivalent LOD score of 5.25).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3.<span style="mso-spacerun: yes"> </span>At this high magnification, individual genes are distinct. They are color coded by their density of SNPs. Bright orange represents those genes that have a high SNP density (C57BL/6J versus DBA/2J), black represents genes with low SNP density. Roll the cursor over a gene block and its name will pop up, along with information on exon number.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>4.<span style="mso-spacerun: yes"> </span>Beneath the physical map you will find an INTERVAL ANALYST table that lists information on known genes in the region on which you have zoomed the Physical Map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>5.<span style="mso-spacerun: yes"> </span>As always: error-checking is important. Some genes may be missing from the Interval Analyst (recent additions or errors of omission). In this case the Zranb1 gene that is located just proximal to Ctbp2 is not listed in the INTERVAL ANALYST. Double-check the interval using the Genome Browser links (blue and beige horizontal bars) at the top of the PHYSICAL MAP.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_image107.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_image107.png new file mode 100755 index 00000000..0e63f836 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_image107.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_image108.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_image108.png new file mode 100755 index 00000000..3c44c2ab --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_image108.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_notes_pane.htm new file mode 100755 index 00000000..010f3332 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The map on the top has an X-axis scale based on frequency of recombinations events between markers (B to D transitions, see slide 19 for a color-coded example). These so-called genetic maps are scaled in centimorgan (recombinations per 100 gametes). In contrast, the physical map shown below the genetic map has an X-axis scale based on DNA length measured in nucleotides or base-pairs. Notice the large difference between the two maps in the size of Chr 19 (large on the genetic scale but small on the physical scale).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Also notice the large difference in the width of the chromosome 7 QTL peak. In mice, recombinations occur with higher frequency toward the telomeric side (righ sidet) of each chromosome. As a result, genetic maps are stretched out more toward the telomere relative to a physical map. The QTL on distal Chr 7 is therefore actually more precisely mapped than might appear looking at the genetic map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The physical scale is becoming more useful than the genetic scale primarily because many other data types can be easily superimposed on a physical map. You will see more examples in the next several slides.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024.htm new file mode 100755 index 00000000..bf2b9b3c --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024.htm @@ -0,0 +1,167 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Evaluating Ctbp2 as a candidate QTL for App"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0024.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Evaluating </span><span style='font-family:Verdana;font-size:64%'><i>Ctbp2</i></span><span style='font-family:Verdana;font-size:64%'> as a candidate QTL for </span><span style='font-family:Verdana;font-size:64%'><i>App</i></span><span style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display: none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.94 * g_height; myleft = 0.03 * g_width; myheight = 0.04 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.03 * g_width; +yy = 0.94 * g_height; +ht = 0.04 * g_height; +wd = 0.96 * g_width; +document.write( +'<img border=0 src="slide0010_image082.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.03 * g_width; myheight = 0.4 * g_height; mywidth = 0.48 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.03 * g_width; +yy = 0.07 * g_height; +ht = 0.4 * g_height; +wd = 0.48 * g_width; +document.write( +'<img border=0 src="slide0010_image083.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.52 * g_height; myleft = 0.55 * g_width; myheight = 0.37 * g_height; mywidth = 0.35 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.33 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>This is</span><span style='font-size:233%;color:#E9EB5D'><i> the </i></span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.34 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2 </i></span><span style='font-size:233%;color:#E9EB5D'>cis QTL, </span></span></layer><script> + mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.35 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>but is detected </span></span></layer><script> + mytop = 0.18 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.33 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>only in the </span></span></layer><script> + mytop = 0.25 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.35 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>Rosen striatum </span></span></layer><script> + mytop = 0.31 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.33 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>data set.</span><span style='font-size:233%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0.56 * g_width; myheight = 0.12 * g_height; mywidth = 0.48 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.45 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>This is</span><span style='font-size:233%;color:#E9EB5D'><i> the App QTL </i></span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.48 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>in the INIA data set. </span><span style='font-size:233%;color:#E9EB5D;mso-special-format: lastCR;display:none'><i><br> </i></span></span></layer></div> </layer><script> + mytop = 0.39 * g_height; myleft = 0.03 * g_width; myheight = 0.53 * g_height; mywidth = 0.48 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.03 * g_width; +yy = 0.39 * g_height; +ht = 0.53 * g_height; +wd = 0.48 * g_width; +document.write( +'<img border=0 src="slide0010_image084.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.35 * g_width; myheight = 0.72 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.35 * g_width; +yy = 0.1 * g_height; +ht = 0.72 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0010_image085.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.31 * g_width; myheight = 0.72 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.31 * g_width; +yy = 0.1 * g_height; +ht = 0.72 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0010_image086.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>This slide illustrates one reason why Ctbp2 should be considered a high priority positional candidate gene that may modulate the expression level of App.<span style="mso-spacerun: yes"> </span>Ctbp2 is a strong cis QTL in some brain regions (here the data are taken from the striatum).<span style="mso-spacerun: yes"> </span>If Ctbp2 contains variants that modulate its own expression then these expression differences may produce many downstream effects. Of course, we now want to know much more about the known biology of Ctbp2. What kind of gene is it? To begin to answer that question we can use a number of resources listed in the LINKS page.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Verdana size=3> The App QTL is bimodal. Perhaps there are actually two causal factors in this region--one close to 123 Mb and the other close to 127 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. The precision of QTL mapping depends on several factors, including the effect size and interactions among QTLs modulating a trait, the number of genetic individuals that are studied, and the distribution of recombinations in the study population.<span style="mso-spacerun: yes"> </span>In the case above, the QTL(s) are likely to be confined to the interval from 120 to 132 Mb. The bootstrap test (yellow bars shown in some of the previous slides) can be usual for estimating the consistency of QTL peaks.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_image109.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_image109.png new file mode 100755 index 00000000..c0174c3f --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_image109.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_image111.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_image111.png new file mode 100755 index 00000000..9a3e3264 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_image111.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_notes_pane.htm new file mode 100755 index 00000000..e6f07dec --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Physical map of variation in App expression in brain on distal Chr 7 (a blow up of the whole-genome map on the previous slide).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Verdana size=2> You can now see that the X-axis is on a physical scale of megabases (Mb). The QTL peak is roughly between 120 and 132 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2. The small irregular colored blocks and marks toward the top of the map mark the locations of genes superimposed on the physical map. Neighboring genes are offset slightly in the vertical axis for display purpose. Note one region of very high gene density from about 120 to 123 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>3. The orange hash marks along the X-axis represent the number of single nucleotide polymorphisms that distinguish the two parental strains (C57BL/6J and DBA/2J) from each other. We call this the SNP seismograph track (see Glossary for more details). Regions with low numbers of SNP have closely matched sequences and are less likely to contain QTLs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>4. As before, the thin red line shows the additive effect size. By convention the positive values signify the D alleles are associated with higher expression of App in this region of Chr 7 than the B alleles. The maximum effect size is about +0.20 log2 expression units per D allele. The differences been the BB and DD genotypes (BB and DD because each strain has two alleles; one per chromosome) is therefore about 2^0.4 = 1.32; or a 32% increment in DD relative to BB at this locus.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>5. If you scroll just under the Physical Map you will see text that reads ÒDISPLAY from XXX Mb TO YYY MbÉ..Ó<span style="mso-spacerun: yes"> </span>These physical maps are zoomable, a feature we will exploit to evaluate candidate genes in this QTL interval.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025.htm new file mode 100755 index 00000000..e9ce598f --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025.htm @@ -0,0 +1,104 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Evaluating Ctbp2 using other resources"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0025.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Evaluating </span><span style='font-family:Verdana;font-size:64%'><i>Ctbp2</i></span><span style='font-family:Verdana;font-size:64%'> using other resources</span><span style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display: none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.01 * g_width; myheight = 0.53 * g_height; mywidth = 0.48 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.1 * g_height; +ht = 0.53 * g_height; +wd = 0.48 * g_width; +document.write( +'<img border=0 src="slide0011_image087.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.4 * g_height; myleft = 0.19 * g_width; myheight = 0.54 * g_height; mywidth = 0.78 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.19 * g_width; +yy = 0.4 * g_height; +ht = 0.54 * g_height; +wd = 0.78 * g_width; +document.write( +'<img border=0 src="slide0011_image088.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Ctbp2 should also be considered a high priority biological candidate gene responsible for modulating App expression levels. The C-terminal binding protein 2 is a transcriptional co-repressor also known as Ribeye.</font><font face=Times-Roman size=3> The gene produces two transcripts encoding distinct proteins. The short form is a transcriptional repressor that binds a Pro-X-Asp-Leu-Ser peptide motif and interacts with several transcription factors including EVI1, ZFPM1, and ZFHX1A (aka TCF8, deltaEF1). The longer isoform is a major component of specialized synapses in photoreceptors. Both proteins contain a NAD+ binding domain similar to NAD+-dependent 2-hydroxyacid dehydrogenases.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. To find out more about CTBP2 protein and the Ctbp2 gene, link to iHOP at http://www.pdg.cnb.uam.es/UniPub/iHOP/ and type in CTBP2</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Try Arrowsmith at http://arrowsmith.psych.uic.edu/cgi-test/arrowsmith_uic/pubsmith.cgi</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. Both APP and CTBP2 are involved in oxidoreducatase activity or Notch signaling. To establish this common gene ontology visit NCBI<span style="mso-spacerun: yes"> </span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene and enter each gene symbol.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. You can get interesting hints regarding Ctbp2 expression partners by examining the genetic correlations between Ctbp2 probe set 1422887_a_at and all other transcripts on the M430 Affymetrix array. Use the Striatum data set because we already know from previous work (the previous slide) that this gene is a cis QTL.<span style="mso-spacerun: yes"> </span>You should be able to show that Ctbp2 and Notch3 have antagonistic expression patterns in striatum. The negative genetic correlation with E2f4 is even stronger. The transcript also has a high positive genetic correlation with Rdh14. Of particular interest with respect to APP protein processing, Ctbp2 covaries positively with Bace2 (the transcript of the beta site APP-cleaving enzyme 2).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025_image112.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025_image112.png new file mode 100755 index 00000000..14e3fbe5 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025_image112.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025_image113.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025_image113.png new file mode 100755 index 00000000..ec9fff87 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025_image113.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025_notes_pane.htm new file mode 100755 index 00000000..19825b0d --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4><b>Evaluating candidate genes (CHECKED BOXES) responsible for variability in APP expression:</b></font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>A large number of genes are usually in the QTL interval and are therefore POSITIONAL CANDIDATES, but they will differ greatly in their biological and bioinformatic plausibility. Assume that the QTL has been located between 119 and 131 Mb (12 Mb). There will typically be 12 to 15 genes per Mb, so we might need to evaluate several hundred positional candidates. In this particular case there are about 100 known genes in this interval. Eight of these are highlighted in the table above with check marks in the boxes to the left.<span style="mso-spacerun: yes"> </span>We need to highlight and objectively score the biologically relevant subset of all 100 positional candidate genes. We could look through gene ontologies and expression levels to help us shorten the list. An alternate way available using WebQTL is to generate a list of those genes in this interval that have transcripts that co-vary in expression with App expression. That is what the table shows.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. To replicate this table go back to the Trait Data and Analysis Form. Choose to sort correlations by POSITION and select RETURN = 500. Then scroll down the list to Chr 7 and review the subset of positional candidates that share expression with App. You should see a list similar to that shown above. Gtf3c1 is a good biological candidate and has a high covariation in expression with App.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>2. Caveat:<span style="mso-spacerun: yes"> </span>Of course, the gene or genes that control App expression may not be in this list. A protein coding difference might be the ultimate cause of variation in App transcript level and the expression covariation might be close to zero. Our list may also simply be missing the right transcript since the microarray is not truly comprehensive. Furthermore, even if the list contains the QT gene, an expression difference may only have been expressed early in development or even in another tissue such as liver. While it is important to recognize these caveats, it is equally important to devise a rational way to rank candidates given existing data. Coexpression is one of several criteria used to evaluate positional candidates. We will see others in the next slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>3. We can also assess the likelihood that candidates contain functional polymorphism in promoters and enhancers that affect their expression simply by mapping the transcripts of all candidate genes to see if they Òmap backÓ to the location of gene itself. A transcript that maps to its own location is referred to as a cis QTL. We essentially ask: Which of the the transcripts listed in the Correlation Table above (from Gtf3c1 to Zranb1) has variation in expression that maps to Chr 7 at about 120 Mb?<span style="mso-spacerun: yes"> </span>The logic of this search is that if a gene controls the level of its own expression it is also much more likely to generate other downstream effects. The Gtf3c1 transcript is a weak cis QTL with a local LRS maximum of about 7.0 (D alleles are high). That is just about sufficient to declare it to be a cis QTL. [No whole genome correction is required and a point-wise p-value of 0.05 is the appropriate test. A p-value of 0.05 is roughly equivalent to an LRS of 6.0 (LOD = 1.3).]</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026.htm new file mode 100755 index 00000000..2ef9b9ff --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026.htm @@ -0,0 +1,139 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0026.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; 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+</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0'><span style='mso-special-format:nobullet;display: none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Summary of Part 2</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0.05 * g_width; myheight = 0.31 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.87 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * g_height; mywidth = 0.84 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.96%;font-family:Arial'>1.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Covered the basics of QTL analysis and mapping.<br> </span></span></layer></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.87 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * g_height; mywidth = 0.84 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.96%;font-family:Arial'>2.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Reviewed difference between genetic and physical maps.<br> </span></span></layer></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.13 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.55%;font-family:Arial'>3.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Discussed interpreting features of QTL maps including the LRS function, </span></span></layer><script> + mytop = 0.04 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * g_height; mywidth = 0.92 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'>the additive effect function, the bootstrap bars, and the permutation </span></span></layer><script> + mytop = 0.09 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * g_height; mywidth = 0.84 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'>thresholds.<br> </span></span></layer></div> </layer><script> + mytop = 0.22 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * g_height; mywidth = 0.86 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.89%;font-family:Arial'>4.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Illustrated techniques to generate a list of positional candidates.<br> </span></span></layer></div> </layer><script> + mytop = 0.26 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.87 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * g_height; mywidth = 0.84 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.96%;font-family:Arial'>5.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Discussed some factors used to evaluate candidate genes.</span></span></layer></div> </layer></div> </layer><script> + mytop = 0.58 * g_height; myleft = 0.05 * g_width; myheight = 0.22 * g_height; mywidth = 1.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'>What does a QTL signify? A good QTL is a claim that a particular </span></span></layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 1.02 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'>chromosomal region contains a causal source of variation in the phenotype. </span></span></layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 1.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'>The importance of this hypothesis depends on the quality and relevance of the </span></span></layer><script> + mytop = 0.13 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'>phenotype and the statistical strength of the QTL. As usual, test and be </span></span></layer><script> + mytop = 0.17 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'>skeptical.</span></span></layer></div> </layer></div> </LAYER> +<script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image114.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image114.png new file mode 100755 index 00000000..93d21c90 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image114.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image115.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image115.png new file mode 100755 index 00000000..fdc27d23 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image115.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image116.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image116.png new file mode 100755 index 00000000..d2cb5ee3 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image116.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_notes_pane.htm new file mode 100755 index 00000000..d335b732 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Even higher blow-up of part of the Chr 7 physical map of variation in App expression in brain.<span style="mso-spacerun: yes"> </span>The QTL region actually extends from about 119 to 129.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. As mentioned in the previous slide another important approach to ranking candidates is based on the number of sequence variants that distinguish the parental strains. If we were sure that the sequences of the gene, its promoter, and its enhancers were identical between the strains then we could discount--but not eliminate--that gene as a candidate. The Gtf3c1 candidate almost falls into this category: of 663 known SNPs in and around this gene, only four differ between C57BL/6J and DBA/2J. Gtf3c1 is essentially identical-by-descent in these strains and is a less likely candidate. In contrast, if the two alleles of the gene have dozens of functional variants in exons, promoters, enhancers, and splice sites, then it becomes a higher priority candidate.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Of course it only takes a single critical sequence variant to generate downstream effects. The argument above is really about the prior probabilities. Where would you place your bets given the information at hand?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2.<span style="mso-spacerun: yes"> </span>If you scroll down the INTERVAL ANALYST you will find that Ctbp2 is a particularly interesting candidate that contains lots of SNPs (n = 75 and a SNP density of 0.55 SNP/Kb). Ctbp2 is also closer to our QTL peak than was Gtf3c1. Not only does Ctbp2 contain lots of SNPs but it is also is associated with a powerful cis QTL with an LRS of 24.2 (divide by 4.61 to get the equivalent LOD score of 5.25).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>3.<span style="mso-spacerun: yes"> </span>At this high magnification, individual genes are distinct. They are color coded by their density of SNPs. Bright orange represents those genes that have a high SNP density (C57BL/6J versus DBA/2J), black represents genes with low SNP density. Roll the cursor over a gene block and its name will pop up, along with information on exon number.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>4.<span style="mso-spacerun: yes"> </span>Beneath the physical map you will find an INTERVAL ANALYST table that lists information on known genes in the region on which you have zoomed the Physical Map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>5.<span style="mso-spacerun: yes"> </span>As always: error-checking is important. Some genes may be missing from the Interval Analyst (recent additions or errors of omission). In this case the Zranb1 gene that is located just proximal to Ctbp2 is not listed in the INTERVAL ANALYST. Double-check the interval using the Genome Browser links (blue and beige horizontal bars) at the top of the PHYSICAL MAP.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027.htm new file mode 100755 index 00000000..c553bae9 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027.htm @@ -0,0 +1,115 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Test Questions"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0027.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Test Questions</span><span style='font-family:Verdana;font-size:73%;mso-special-format: lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.11 * g_height; myleft = 0.04 * g_width; myheight = 0.06 * g_height; mywidth = 1.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-size:233%;color:#E9EB5D'>1. Evaluate candidates for the Chr 3 </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span style='font-size:233%;color:#E9EB5D'> QTL.</span><span style='font-size:233%; color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </layer><script> + mytop = 0.24 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>2. Do </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span style='font-size: 233%;color:#E9EB5D'> and </span><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span style='font-size:233%;color:#E9EB5D'> expression share any </span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>other QTLs beside that on Chr 7?</span><span style='font-size:233%;color:#E9EB5D; mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer><script> + mytop = 0.43 * g_height; myleft = 0.04 * g_width; myheight = 0.19 * g_height; mywidth = 1.02 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.02 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>3. Can you exploit literature mining tools to </span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>find a strong relationship between </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span style='font-size:233%;color:#E9EB5D'> and </span></span></layer><script> + mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span style='font-size:233%;color:#E9EB5D'>? </span><span style='font-size:233%; color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer><script> + mytop = 0.69 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 1.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>4. Why might the cis QTL for </span><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span style='font-size:233%;color:#E9EB5D'> expression </span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>only be detected in the striatum data set?</span><span style='font-size:233%; color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </LAYER> +<script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image118.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image118.png new file mode 100755 index 00000000..cf5f70f7 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image118.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image119.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image119.png new file mode 100755 index 00000000..a5886d21 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image119.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image120.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image120.png new file mode 100755 index 00000000..7eb77319 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image120.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image121.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image121.png new file mode 100755 index 00000000..99f4d04d --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image121.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image122.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image122.png new file mode 100755 index 00000000..ac87ce02 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image122.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_notes_pane.htm new file mode 100755 index 00000000..26d15c0e --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>This slide illustrates one reason why Ctbp2 should be considered a high priority positional candidate gene that may modulate the expression level of App.<span style="mso-spacerun: yes"> </span>Ctbp2 is a strong cis QTL in some brain regions (here the data are taken from the striatum).<span style="mso-spacerun: yes"> </span>If Ctbp2 contains variants that modulate its own expression then these expression differencess may produce many downstream effects. Of course, we now want to know much more about the known biology of Ctbp2. What kind of gene is it? To begin to answer that question we can use a number of resources listed in the LINKS page.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Verdana size=2> The App QTL is bimodal. Perhaps there are actually two causal factors in this region--one close to 123 Mb and the other close to 127 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2. The precision of QTL mapping depends on several factors, including the effect size and interactions among QTLs modulating a trait, the number of genetic individuals that are studied, and the distribution of recombinations in the study population.<span style="mso-spacerun: yes"> </span>In the case above, the QTL(s) are likely to be confined to the interval from 120 to 132 Mb. The bootstrap test (yellow bars shown in some of the previous slides) can be usual for estimating the consiistency of QTL peaks.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028.htm new file mode 100755 index 00000000..67711e7c --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028.htm @@ -0,0 +1,112 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Contact for comments and improvements:"> <style media=print> <!--.sld {left:0px !important; 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myleft = 0.06 * g_width; myheight = 0.24 * g_height; mywidth = 0.9 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.24 * g_height; mywidth = 0.87 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.87 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:82%'>rwilliam@nb.utmem.edu<br> </span></span></layer><script> + mytop = 0.08 * g_height; myleft = 0.04 * g_width; myheight = 0.07 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:82%'><br> </span></span></layer><script> + mytop = 0.16 * g_height; myleft = 0.04 * g_width; myheight = 0.07 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:82%;mso-special-format:lastCR; display:none'><br> </span></span></layer></div> </layer></div> </layer><script> + mytop = 0.27 * g_height; myleft = 0.09 * g_width; myheight = 0.07 * g_height; mywidth = 0.5 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:300%; color:#E9EB5D'>kmanly@utmem.edu</span></div> </layer><script> + mytop = 0.83 * g_height; myleft = 0.04 * g_width; myheight = 0.15 * g_height; mywidth = 1.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'>The </span><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'><i>App</i></span><span style='font-family:"Gill Sans"; font-size:200%;color:#E9EB5D'> findings reviewed in this presentation are part of an </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'>ongoing study by R. Williams. R. Homayouni, and R. Clark (July 15, </span></span></layer><script> + mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'>2005)</span><span style='font-family:"Gill Sans";font-size:300%; color:#E9EB5D;mso-special-format:lastCR;display:none'><br> </span></span></layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>END</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_image123.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_image123.png new file mode 100755 index 00000000..a6ca39ae --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_image123.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_image124.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_image124.png new file mode 100755 index 00000000..c17a41bc --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_image124.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_notes_pane.htm new file mode 100755 index 00000000..3693ce68 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Ctbp2 should also be considered a high priority biological candidate gene responsible for modulating App expression levels. The<span style="mso-spacerun: yes"> </span>C-terminal binding protein 2 is a transcriptional co-repressor also known as Ribeye.</font><font face=Times-Roman size=2> The gene produces two transcripts encoding distinct proteins. The short form is a transcriptional repressor that binds a Pro-X-Asp-Leu-Ser peptide motif common to adenoviral oncoprotein E1a and a related motif in BKLF. This short form also interacts<span style="mso-spacerun: yes"> </span>with several transcription factors including EVI1, ZFPM1, and<span style="mso-spacerun: yes"> </span>ZFHX1A (aka TCF8, deltaEF1). The longer isoform is a major component of specialized synapses in photoreceptors. Both proteins contain a NAD+ binding domain similar to NAD+-dependent 2-hydroxyacid dehydrogenases.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>1. To find out more about CTBP2 protein and the Ctbp2 gene, link to iHOP at http://www.pdg.cnb.uam.es/UniPub/iHOP/ and type in CTBP2</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Try Arrowsmith at http://arrowsmith.psych.uic.edu/cgi-test/arrowsmith_uic/pubsmith.cgi</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2. Both APP and CTBP2 are involved in oxidoreducatase activity or Notch signalling. To estabilish this common gene ontology visit NCBI<span style="mso-spacerun: yes"> </span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene<span style="mso-spacerun: yes"> </span>and enter each gene symbol.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>3. You can get intersting hints regarding Ctbp2 expression partners by examining the genetic correlations between Ctbp2 probe set 1422887_a_at and all other transcripts on the M430 Affymetrix array. Use the Striatum data set because we already know from previous work (the previous slide) that this gene is a cis QTL.<span style="mso-spacerun: yes"> </span>You should be able to show that Ctbp2 and Notch3 have antagonistic expression patterns in striatum. The negative genetic correlation with E2f4 is even stronger. The transcript also has a high positive genetic correlation with Rdh14. Of particualr interest with respect to APP protein processing, Ctbp2 covaries positiviely with Bace2 (the transcript of the beta site APP-cleaving enzyme 2).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0029.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0029.htm new file mode 100755 index 00000000..74ec8342 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0029.htm @@ -0,0 +1,34 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: The GeneNetwork and WebQTL : PART 2 link to www.genenetwork.org"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript> + if ( parent.base.msie < 0 ) { + document.captureEvents(Event.MOUSEDOWN); + document.captureEvents(Event.KEYPRESS); + document.onkeypress = _KPH; + document.onmousedown = _KPH; + } + +function restore() { + if ( parent.base.msie < 0 ) + self.location.reload(); +} +</script> +<script language=JavaScript> +function flatLoad() { +if ( !parent.IsFullScrMode() ) + parent.base.highlite(); +DoOnLoad(); + + + if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed ) + parent.NavPopup.focus(); + else + self.focus(); + parent.base.SldUpdated( "slide0029.htm" ); + } + </script><script language=JavaScript><!-- +function DoOnLoad() { + }//--> +</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0001.gif border=0 usemap="#Slide0001.gif_map"></center> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0030.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0030.htm new file mode 100755 index 00000000..5562bbe5 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0030.htm @@ -0,0 +1,34 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! 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top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jul-18-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0043.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.14 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.9 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56'><span style='mso-special-format:nobullet; display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> and </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>Atcay</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> transcript scatterplot </span></div> </layer></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0.05 * g_width; myheight = 0.91 * g_height; mywidth = 0.66 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.05 * g_width; +yy = 0.08 * g_height; +ht = 0.91 * g_height; +wd = 0.66 * g_width; +document.write( +'<img border=0 src="slide0012_image026.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>By clicking on the CORRELATION of the Atcay transcript to the App transcript, you can generate a Correlation plot between these two transcripts. In this App and Atcay scatterplot, each point is a strain mean value. For example, BXD33 and BXD8 have low App and Atcay expressions. The two parental strains and the F1 are also included in this plot.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0044.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0044.htm new file mode 100755 index 00000000..ec5c2e3c --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0044.htm @@ -0,0 +1,93 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jul-18-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0044.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.14 * g_height; mywidth = 0.99 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56'><span style='mso-special-format:nobullet; display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> transcript and eight of its neighbors</span></div> </layer></div> </layer><script> + mytop = 0.09 * g_height; myleft = 0.02 * g_width; myheight = 0.9 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.02 * g_width; +yy = 0.09 * g_height; +ht = 0.9 * g_height; +wd = 0.83 * g_width; +document.write( +'<img border=0 src="slide0013_image027.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>A group of traits from many different databases can be selected and brought together for joint analysis. In this case all of the content of the BXD SELECTIONS is from a single BRAIN database, the top 20 neighbors of the App transcript from the Correlation Results table. Eight of these neighbors plus App is shown in the slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Helvetica size=3>All of items in the BXD SELECTIONS were selected using the SELECT ALL button</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. The buttons at the top (and bottom) of this page can do some cool stuff. We will work with NETWORK GRAPH first.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. Think of the SELECTIONS as your shopping cart. You go to different aisles in the supermarket to acquire different types of items of interest. These could include transcripts, classical phenotypes (longevity, brain weight, prepulse inhibition, iron levels in midbrain). ÒChecking outÓ in this case involves doing some analysis with the items in the cart.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>4. Different tools handle different numbers of items. Most will handle up to 100 traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0045.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0045.htm new file mode 100755 index 00000000..4e705866 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0045.htm @@ -0,0 +1,118 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jul-18-05: App transcript coexpression neighborhood"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0045.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.82 * g_height; myleft = 0.04 * g_width; myheight = 0.18 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div></div> </layer><script> + mytop = -0.02 * g_height; myleft = 0 * g_width; myheight = 0.12 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.02 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%'><span style='font-size:82%'><i>App</i></span><span style='font-size:82%'> transcript coexpression neighborhood</span><span style='mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.37 * g_height; myleft = 0.01 * g_width; myheight = 0.62 * g_height; mywidth = 0.97 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.37 * g_height; +ht = 0.62 * g_height; +wd = 0.97 * g_width; +document.write( +'<img border=0 src="slide0014_image029.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.11 * g_height; myleft = 0.01 * g_width; myheight = 0.25 * g_height; mywidth = 0.79 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.11 * g_height; +ht = 0.25 * g_height; +wd = 0.79 * g_width; +document.write( +'<img border=0 src="slide0014_image031.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.81 * g_width; myheight = 0.09 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.81 * g_width; +yy = 0.1 * g_height; +ht = 0.09 * g_height; +wd = 0.18 * g_width; +document.write( +'<img border=0 src="slide0014_image033.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Output of the Network Graph. Warm colors (orange and red) are positive correlations above 0.5 whereas cool colors (green and blue) are negative correlations. Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Helvetica size=3> All of the nodes (gene/transcripts) on this graph are clickable.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. For this graph the App expression values have ÒrevertedÓ to their pre-Windsorized values.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. To generate this graph, we used the default setting:<span style="mso-spacerun: yes"> </span>Size of 16 by 16 inches; Gene Symbols; Don't Show Correlations; Use curved lines (aka ÒedgesÓ).</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0046.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0046.htm new file mode 100755 index 00000000..93429543 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0046.htm @@ -0,0 +1,104 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jul-18-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0046.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.14 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0'><span style='mso-special-format:nobullet;display: none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Correlations of </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> with classical traits</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.28 * g_height; myleft = 0.04 * g_width; myheight = 0.7 * g_height; mywidth = 0.78 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.04 * g_width; +yy = 0.28 * g_height; +ht = 0.7 * g_height; +wd = 0.78 * g_width; +document.write( +'<img border=0 src="slide0015_image034.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0.04 * g_width; myheight = 0.19 * g_height; mywidth = 0.33 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.04 * g_width; +yy = 0.08 * g_height; +ht = 0.19 * g_height; +wd = 0.33 * g_width; +document.write( +'<img border=0 src="slide0015_image035.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Going back to the Trait Data and Analysis Form window, we have computed the correlations between strain variation in App expression level and other classical phenotypes that have already been measured in many of the same BXD strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Helvetica size=3>The number of common strains varies widely--in this case from 14 to 23 strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. We can add these traits (four are selected) to our BXD SELECTIONS window.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0047.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0047.htm new file mode 100755 index 00000000..e7568e44 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0047.htm @@ -0,0 +1,93 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jul-18-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0047.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 0.99 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0'><span style='mso-special-format:nobullet;display: none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Network Graph of </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> with classical traits</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0.03 * g_width; myheight = 0.9 * g_height; mywidth = 0.88 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.03 * g_width; +yy = 0.08 * g_height; +ht = 0.9 * g_height; +wd = 0.88 * g_width; +document.write( +'<img border=0 src="slide0016_image036.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>We have computed the Network Graph, now using other types of traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Saline Hot Plate Latency is the green node labeled 10020.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Freezing (fear) is the green node labeled 10447.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0048.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0048.htm new file mode 100755 index 00000000..f36b1e25 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0048.htm @@ -0,0 +1,151 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jul-18-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0048.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.01 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0'><span style='mso-special-format:nobullet;display: none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Summary of Part 1:</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.08 * g_width; myheight = 0.47 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.9 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.88 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.84%;font-family:Arial'>1.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You have learned the basics about searching for traits<br> </span></span></layer></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.85 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-3.03%;font-family:Arial'>2.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know some methods to check data quality<br> </span></span></layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.85 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-3.03%;font-family:Arial'>3.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to edit bad or suspicious data<br> </span></span></layer></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.9 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.88 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.85%;font-family:Arial'>4.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to review the basic statistics of a trait<br> </span></span></layer></div> </layer><script> + mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.74%;font-family:Arial'>5.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to generate a scattergram between two </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>traits using the Traits Correlation tool<br> </span></span></layer></div> </layer><script> + mytop = 0.31 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.56%;font-family:Arial'>6.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to add items to your SELECTIONS window<br> </span></span></layer></div> </layer><script> + mytop = 0.37 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.97 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.57%;font-family:Arial'>7.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to generate a Network Graph of traits that </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>co-vary. </span></span></layer></div> </layer></div> </layer><script> + mytop = 0.67 * g_height; myleft = 0.05 * g_width; myheight = 0.26 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>What does genetic covariance mean? The genetic covariance can </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>be functional and mechanistic, but it can also be due to linkage </span></span></layer><script> + mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>disequilibrium. Finally, it can be due to sampling error or poor </span></span></layer><script> + mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.92 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>experimental design. Evaluate the biological plausibility of </span></span></layer><script> + mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>correlations. Test and be skeptical.</span></span></layer></div> </layer></div> </LAYER> +<script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0049.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0049.htm new file mode 100755 index 00000000..9d36600a --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0049.htm @@ -0,0 +1,155 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jul-18-05: The GeneNetwork and WebQTL : PART 2 link to www.genenetwork.org"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0049.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0.02 * g_width; myheight = 0.18 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.02 * g_height; myleft = 0 * g_width; myheight = 0.13 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-277 0 -1";mso-margin-left-alt:232; mso-text-indent-alt:0;mso-line-spacing:"-277 0 -1";mso-margin-left-alt:232; mso-text-indent-alt:0'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:73%'>The GeneNetwork and WebQTL : PART 2<span style="mso-spacerun: yes"> </span><br> </span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0.04 * g_width; myheight = 0.06 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:73%'>link to www.genenetwork.org</span><span style='font-size:73%;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </layer><script> + mytop = 0.24 * g_height; myleft = 0.05 * g_width; myheight = 0.68 * g_height; mywidth = 0.54 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.42 * g_height; mywidth = 0.52 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.21 * g_height; mywidth = 0.52 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.46 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part 1. How to study </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.41 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>expression variation </span></span></layer><script> + mytop = 0.1 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.47 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>and genetic correlation </span></span></layer><script> + mytop = 0.15 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.41 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>(slides 2–17)<br> </span></span></layer></div> </layer><script> + mytop = 0.25 * g_height; myleft = 0 * g_width; myheight = 0.16 * g_height; mywidth = 0.48 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.46 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part 2. Discovering </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.43 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>upstream modulators </span></span></layer><script> + mytop = 0.1 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.41 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>(slides 18–29)</span></span></layer></div> </layer></div> </layer></div> </layer><script> + mytop = 0.17 * g_height; myleft = 0.74 * g_width; myheight = 0.64 * g_height; mywidth = 0.23 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.74 * g_width; +yy = 0.17 * g_height; +ht = 0.64 * g_height; +wd = 0.23 * g_width; +document.write( +'<img border=0 src="slide0018_image037.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.75 * g_height; myleft = 0.74 * g_width; myheight = 0.14 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:"Arial Rounded MT Bold";font-size:233%;color:#6E6E6E'>RNA</span><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; display:none'><br> </span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.82 * g_height; myleft = 0.04 * g_width; myheight = 0.18 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div></div> </layer><script> + mytop = 0.5 * g_height; myleft = 0.48 * g_width; myheight = 0.13 * g_height; mywidth = 0.25 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.48 * g_width; +yy = 0.5 * g_height; +ht = 0.13 * g_height; +wd = 0.25 * g_width; +document.write( +'<img border=0 src="slide0018_image038.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Part 2: Discovering upstream modulators and quantitative trait loci (QTLs). A quantitative trait locus is a chromosomal region that harbors one or a few polymorphic gene loci that influence a trait. We are going to be looking for QTLs that modulate the steady state expression level of App in the adult mouse forebrain.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0050.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0050.htm new file mode 100755 index 00000000..48469040 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0050.htm @@ -0,0 +1,919 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jul-18-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0050.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; 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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master05_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.92 * g_height; myleft = 0.08 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.02 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-134 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Times;font-size:117%;color:white;display:none'><br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.02 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-134 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Times;font-size:117%;color:white;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.92 * g_height; myleft = 0.35 * g_width; myheight = 0.05 * g_height; mywidth = 0.29 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.02 * g_height; mywidth = 0.29 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Times;font-size:117%; color:white;display:none'><br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.02 * g_height; mywidth = 0.29 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Times;font-size:117%; color:white;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.02 * g_height; myleft = -0.05 * g_width; myheight = 0.11 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-240 0 0";mso-margin-left-alt: 16;mso-text-indent-alt:16'><span style='font-family:Arial;font-size:267%; color:#E9EB5D'>How to make recombinant inbred strains (RI)</span><span style='font-family:Arial;font-size:150%;color:aqua;display:none'><br> </span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0.06 * g_width; myheight = 0.03 * g_height; mywidth = 0.92 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-160 0 0";mso-margin-left-alt: 16;mso-text-indent-alt:16'><span style='font-family:Arial;font-size:150%; color:aqua;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.28 * g_height; myleft = 0.45 * g_width; myheight = 0.01 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.45 * g_width; +yy = 0.28 * g_height; +ht = 0.01 * g_height; +wd = 0.18 * g_width; +document.write( +'<img border=0 src="slide0019_image039.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.28 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.28 * g_width; +yy = 0.2 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0019_image040.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0.25 * g_width; myheight = 0.09 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>C57BL/6J (B)<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.3 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.3 * g_width; +yy = 0.2 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0019_image041.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0.62 * g_width; myheight = 0.09 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>DBA/2J (D)<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.66 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.66 * g_width; +yy = 0.2 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0019_image042.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.23 * g_width; myheight = 0.01 * g_height; mywidth = 0.5 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.23 * g_width; +yy = 0.35 * g_height; +ht = 0.01 * g_height; +wd = 0.5 * g_width; +document.write( +'<img border=0 src="slide0019_image043.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.24 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.24 * g_width; +yy = 0.35 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0019_image044.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.4 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.4 * g_width; +yy = 0.35 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0019_image045.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.57 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.57 * g_width; +yy = 0.35 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0019_image046.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.74 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.74 * g_width; +yy = 0.35 * g_height; +ht = 0.03 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0019_image047.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.42 * g_height; myleft = 0.05 * g_width; myheight = 0.12 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F1<br> </b></span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format: lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.39 * g_height; myleft = 0.22 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.22 * g_width; +yy = 0.39 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0019_image048.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.39 * g_height; myleft = 0.38 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.38 * g_width; +yy = 0.39 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0019_image049.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.39 * g_height; myleft = 0.55 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.55 * g_width; +yy = 0.39 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0019_image050.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.39 * g_height; myleft = 0.72 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.72 * g_width; +yy = 0.39 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0019_image051.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.43 * g_height; myleft = 0.43 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.43 * g_width; +yy = 0.43 * g_height; +ht = 0.03 * g_height; +wd = 0.11 * g_width; +document.write( +'<img border=0 src="slide0019_image052.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.6 * g_height; myleft = 0.2 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.2 * g_width; +yy = 0.6 * g_height; +ht = 0.03 * g_height; +wd = 0.09 * g_width; +document.write( +'<img border=0 src="slide0019_image053.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.71 * g_height; myleft = 0.58 * g_width; myheight = 0.26 * g_height; mywidth = 0.2 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.03 * g_height; myleft = 0.01 * g_width; myheight = 0.22 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.15 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:117%; color:#FFFF99'><b>20 generations </b></span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:117%; color:#FFFF99'><b>brother-sister </b></span></span></layer><script> + mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:117%; color:#FFFF99'><b>matings</b></span><span style='font-family:Arial;font-size: 233%;color:#FFFF99;display:none'><b><br> </b></span></span></layer></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:233%; color:#FFFF99;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.6 * g_height; myleft = 0.5 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.5 * g_width; +yy = 0.6 * g_height; +ht = 0.03 * g_height; +wd = 0.09 * g_width; +document.write( +'<img border=0 src="slide0019_image054.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.62 * g_height; myleft = 0.54 * g_width; myheight = 0.28 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.54 * g_width; +yy = 0.62 * g_height; +ht = 0.28 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0019_image055.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.61 * g_height; myleft = 0.79 * g_width; myheight = 0.03 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.79 * g_width; +yy = 0.61 * g_height; +ht = 0.03 * g_height; +wd = 0.1 * g_width; +document.write( +'<img border=0 src="slide0019_image056.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.62 * g_height; myleft = 0.83 * g_width; myheight = 0.28 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.83 * g_width; +yy = 0.62 * g_height; +ht = 0.28 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0019_image057.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.92 * g_height; myleft = 0.21 * g_width; myheight = 0.09 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD1</span><span style='font-family:Arial;font-size:150%;color:#484848;display:none'><br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#484848;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.92 * g_height; myleft = 0.51 * g_width; myheight = 0.09 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD2<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.92 * g_height; myleft = 0.8 * g_width; myheight = 0.05 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:"-173 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;mso-line-spacing:"-173 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>BXD80</span></div> </layer></div> </layer><script> + mytop = 0.9 * g_height; myleft = 0.64 * g_width; myheight = 0.17 * g_height; mywidth = 0.17 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.15 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-341 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:300%;color:#FFFF99'>+ É +<br> </span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-341 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:300%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.62 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F2<br> </b></span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format: lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.18 * g_width; myheight = 0.01 * g_height; mywidth = 0.75 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.18 * g_width; +yy = 0.54 * g_height; +ht = 0.01 * g_height; +wd = 0.75 * g_width; +document.write( +'<img border=0 src="slide0019_image058.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.17 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.17 * g_width; +yy = 0.54 * g_height; +ht = 0.03 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0019_image059.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.32 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.32 * g_width; +yy = 0.54 * g_height; +ht = 0.03 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0019_image060.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.48 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.48 * g_width; +yy = 0.54 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0019_image061.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.62 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.62 * g_width; +yy = 0.54 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0019_image062.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.77 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.77 * g_width; +yy = 0.54 * g_height; +ht = 0.04 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0019_image063.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.92 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.92 * g_width; +yy = 0.54 * g_height; +ht = 0.03 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0019_image064.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.44 * g_height; myleft = 0.49 * g_width; myheight = 0.1 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.49 * g_width; +yy = 0.44 * g_height; +ht = 0.1 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0019_image065.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.15 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.15 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0019_image066.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.3 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.3 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0019_image067.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.46 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.46 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0019_image068.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.6 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.6 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0019_image069.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.75 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.75 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0019_image070.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.9 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.9 * g_width; +yy = 0.57 * g_height; +ht = 0.11 * g_height; +wd = 0.04 * g_width; +document.write( +'<img border=0 src="slide0019_image071.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.84 * g_height; myleft = 0.56 * g_width; myheight = 0.01 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.56 * g_width; +yy = 0.84 * g_height; +ht = 0.01 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0019_image072.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.8 * g_height; myleft = 0.25 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.25 * g_width; +yy = 0.8 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0019_image073.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.84 * g_height; myleft = 0.86 * g_width; myheight = 0.02 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.86 * g_width; +yy = 0.84 * g_height; +ht = 0.02 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0019_image074.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.75 * g_height; myleft = 0.01 * g_width; myheight = 0.13 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'><b>BXD RI<br> </b></span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'><b>Strain set<br> </b></span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.01 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.12 * g_height; myleft = 0.14 * g_width; myheight = 0.06 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.14 * g_width; +yy = 0.12 * g_height; +ht = 0.06 * g_height; +wd = 0.1 * g_width; +document.write( +'<img border=0 src="slide0019_image075.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.76 * g_width; myheight = 0.08 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.76 * g_width; +yy = 0.1 * g_height; +ht = 0.08 * g_height; +wd = 0.14 * g_width; +document.write( +'<img border=0 src="slide0019_image076.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.17 * g_width; myheight = 0.13 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>fully<br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>inbred<br> </span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.38 * g_height; myleft = 0.02 * g_width; myheight = 0.09 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>isogenic<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.54 * g_height; myleft = 0.01 * g_width; myheight = 0.13 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>hetero-<br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>geneous<br> </span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.74 * g_height; myleft = 0.29 * g_width; myheight = 0.21 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.19 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.15 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>Recombined </span></span></layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>chromosomes </span></span></layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>are needed for </span></span></layer><script> + mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>mapping<br> </span></span></layer></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.25 * g_width; myheight = 0.09 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>female<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.64 * g_width; myheight = 0.09 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>male<br> </span></div> </layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.3 * g_height; myleft = 0.78 * g_width; myheight = 0.09 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:117%;color:#FFFF99'>chromosome pair</span><span style='font-family:Arial;font-size:150%;color:#FFFF99; display:none'><br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.31 * g_height; myleft = 0.65 * g_width; myheight = 0.02 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.65 * g_width; +yy = 0.31 * g_height; +ht = 0.02 * g_height; +wd = 0.12 * g_width; +document.write( +'<img border=0 src="slide0019_image077.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.86 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.12 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%; color:#E9EB5D'>Inbred<br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%; color:#E9EB5D'>Isogenic<br> </span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%; color:#E9EB5D'>siblings</span><span style='font-family:Arial;font-size:117%; color:aqua;display:none'><br> </span></div> </layer><script> + mytop = 0.09 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%; color:aqua;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.79 * g_height; myleft = 0.83 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.83 * g_width; +yy = 0.79 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0019_image078.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.84 * g_height; myleft = 0.83 * g_width; myheight = 0.02 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.83 * g_width; +yy = 0.84 * g_height; +ht = 0.02 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0019_image079.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.79 * g_height; myleft = 0.53 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.53 * g_width; +yy = 0.79 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0019_image080.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.83 * g_height; myleft = 0.53 * g_width; myheight = 0.01 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.53 * g_width; +yy = 0.83 * g_height; +ht = 0.01 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0019_image081.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.8 * g_height; myleft = 0.23 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.23 * g_width; +yy = 0.8 * g_height; +ht = 0.11 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0019_image082.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.18 * g_height; myleft = 0.43 * g_width; myheight = 0.09 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:"-341 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;mso-line-spacing:"-341 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Arial;font-size:300%; color:aqua'>B</span><span style='font-family:Arial;font-size:300%;color:#FFFF99'>X</span><span style='font-family:Arial;font-size:300%;color:#FF1911'>D</span></div> </layer></div> </layer><script> + mytop = 0.27 * g_height; myleft = 0.32 * g_width; myheight = 0.04 * g_height; mywidth = 0.31 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.32 * g_width; +yy = 0.27 * g_height; +ht = 0.04 * g_height; +wd = 0.31 * g_width; +document.write( +'<img border=0 src="slide0019_image083.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.66 * g_height; myleft = 0.6 * g_width; myheight = 0.03 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.6 * g_width; +yy = 0.66 * g_height; +ht = 0.03 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0019_image084.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.64 * g_height; myleft = 0.15 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.15 * g_width; +yy = 0.64 * g_height; +ht = 0.05 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0019_image085.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.57 * g_height; myleft = 0.75 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.75 * g_width; +yy = 0.57 * g_height; +ht = 0.05 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0019_image086.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.28 * g_height; myleft = 0.48 * g_width; myheight = 0.08 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.48 * g_width; +yy = 0.28 * g_height; +ht = 0.08 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0019_image087.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.62 * g_height; myleft = 0.23 * g_width; myheight = 0.16 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.23 * g_width; +yy = 0.62 * g_height; +ht = 0.16 * g_height; +wd = 0.03 * g_width; +document.write( +'<img border=0 src="slide0019_image088.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.61 * g_height; myleft = 0.63 * g_width; myheight = 0.08 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.63 * g_width; +yy = 0.61 * g_height; +ht = 0.08 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0019_image089.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The next few slides provide a short introduction to mapping the loci that are responsible for variation in a trait such as App expression level. These modulatory regions of the genome are sometimes called quantitative trait loci or QTLs. You may want to do some independent reading on this topic if this is your first exposure to QTL analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The genetic reference population (GRP) of BXD recombinant inbred strains were originally generated about 25 years ago by Benjamin Taylor at The Jackson Laboratory. He crossed female C57BL/6J mice with male DBA/2J mice to generate the F1 and F2 progeny. At the bottom of this slide we have schematized one chromosome pair from three of the BXD RI strains.<span style="mso-spacerun: yes"> </span>The dashed vertical lines that lead to the final BXD RI lines involve 21 full sib matings (about 7 years of breeding). Some lines die out during inbreeding. For example, there is no longer any BXD3 strain.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. Over the last decade, our group (Lu Lu and Rob Williams) and Jeremy Peirce and Lee Silver at Princeton have enlarged Ben TaylorÕs set. There are now just over 80 BXD strains. They have all been genotyped using about 13,700 markers (SNPs and microsatellites). These markers are used to define the ÒblueÓ and ÒredÓ regions of the chromosomes as shown in the figure above.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. Chromosomes of RI GRPs usually have about 4 times as many recombinations as those of F2 animals. However, unlike an F2, both chromosomes of an RI are identical. Therefore, 50 RI strains contain as many recombinations as 100 F2 animals.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. BXD43 through BXD100 were generated using a special method that resulted in a further doubling of the average recombination density per chromosome. The entire set of 80 BXDs therefore contains as many recombinations as about 260 F2 animals.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0051.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0051.htm new file mode 100755 index 00000000..29b1f60e --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0051.htm @@ -0,0 +1,421 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jul-18-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0051.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.4 * g_height; myleft = 0.73 * g_width; myheight = 0.05 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.73 * g_width; +yy = 0.4 * g_height; +ht = 0.05 * g_height; +wd = 0.14 * g_width; +document.write( +'<img border=0 src="slide0020_image090.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.4 * g_height; myleft = 0.74 * g_width; myheight = 0.07 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Gadget;font-size:150%;color:white'>aa<br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Gadget;font-size:150%;color:white;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0.73 * g_width; myheight = 0.05 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.73 * g_width; +yy = 0.16 * g_height; +ht = 0.05 * g_height; +wd = 0.14 * g_width; +document.write( +'<img border=0 src="slide0020_image091.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0.74 * g_width; myheight = 0.07 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Gadget;font-size:150%;color:white'>aaaa<br> </span></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Gadget;font-size:150%;color:white;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.71 * g_width; myheight = 0.19 * g_height; mywidth = 0.25 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.24 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.24 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:267%;color:#E2EBF0'>D2 strain</span><span style='font-family:Palatino;font-size:333%;color:#FBFDB8;display:none'><br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-family:Palatino;font-size:333%;color:#FBFDB8;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.43 * g_height; myleft = 0.71 * g_width; myheight = 0.19 * g_height; mywidth = 0.25 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.02 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.24 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.24 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:267%;color:#F6BF69'>B6 strain</span><span style='font-family:Palatino;font-size:333%;color:#F6BF69;display:none'><br> </span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-family:Palatino;font-size:333%;color:#F6BF69;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.17 * g_height; myleft = 0.31 * g_width; myheight = 0.42 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.31 * g_width; +yy = 0.17 * g_height; +ht = 0.42 * g_height; +wd = 0.01 * g_width; +document.write( +'<img border=0 src="slide0020_image092.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.4 * g_height; myleft = 0.31 * g_width; myheight = 0.03 * g_height; mywidth = 0.39 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.31 * g_width; +yy = 0.4 * g_height; +ht = 0.03 * g_height; +wd = 0.39 * g_width; +document.write( +'<img border=0 src="slide0020_image093.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.38 * g_width; myheight = 0.26 * g_height; mywidth = 0.3 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.23 * g_height; mywidth = 0.27 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.13 * g_height; mywidth = 0.27 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-320 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.27 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'><i>amount of </i></span></span></layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.27 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'><i>transcript</i></span><span style='font-family:Palatino;font-size:367%;color:#E9EB5D;display:none'><br> </span></span></layer></div> </layer><script> + mytop = 0.14 * g_height; myleft = 0 * g_width; myheight = 0.09 * g_height; mywidth = 0.27 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-422 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-family:Palatino;font-size:367%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0.72 * g_width; myheight = 0.19 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:267%;color:white'>4 </span><span style='font-size: 233%;color:white'>units</span><span style='font-family:Palatino;font-size:333%; color:#E9EB5D;display:none'><br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-family:Palatino;font-size:333%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.29 * g_height; myleft = 0.72 * g_width; myheight = 0.19 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.02 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:267%;color:white'>2</span><span style='font-size: 233%;color:white'> units</span><span style='font-family:Palatino;font-size: 333%;color:#E9EB5D;display:none'><br> </span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-family:Palatino;font-size:333%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0.31 * g_width; myheight = 0.05 * g_height; mywidth = 0.4 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.31 * g_width; +yy = 0.15 * g_height; +ht = 0.05 * g_height; +wd = 0.4 * g_width; +document.write( +'<img border=0 src="slide0020_image094.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.17 * g_height; myleft = 0.09 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#E2EBF0'>D<br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.17 * g_height; myleft = 0.17 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69'>B<br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.79 * g_height; myleft = 0.05 * g_width; myheight = 0.13 * g_height; mywidth = 1.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.12 * g_height; mywidth = 1.02 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:"-256 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;mso-line-spacing:"-256 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.02 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E2EBF0'>D</span><span style='font-size:233%;color:#E9EB5D'> </span><span style='font-size:200%; color:#E9EB5D'>and </span><span style='font-size:233%;color:#F6BF69'>B</span><span style='font-size:233%;color:#E9EB5D'> </span><span style='font-size:200%; color:#E9EB5D'>may be SNP-like variants in the promoter </span></span></layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 1.02 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:200%;color:#E9EB5D'>itself (cis QTL) or in </span><span style='font-size:200%;color:#EAEC5E'>upstream genes (trans QTLs)</span><span style='font-size:300%;color:#E9EB5D'>.</span></span></layer></div> </layer></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.04 * g_width; myheight = 0.16 * g_height; mywidth = 0.22 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.22 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-233 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-size:200%;color:#E9EB5D'>UPSTREAM<br> </span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.22 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-233 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-size:200%;color:#E9EB5D'>modulators<br> </span></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.01 * g_width; myheight = 0.05 * g_height; mywidth = 0.2 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-233 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-size:200%;color:#E9EB5D; mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.44 * g_width; myheight = 0.17 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:300%;color:#E2EBF0'>High<br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.63 * g_height; myleft = 0.08 * g_width; myheight = 0.17 * g_height; mywidth = 0.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#E2EBF0'>D<br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.63 * g_height; myleft = 0.15 * g_width; myheight = 0.17 * g_height; mywidth = 0.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69'>B<br> </span></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.71 * g_height; myleft = 0.07 * g_width; myheight = 0.12 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D'><i>cis QTL</i></span><span style='font-size:200%;color:#E9EB5D;display:none'><br> </span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.57 * g_height; myleft = -0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = -0.01 * g_width; +yy = 0.57 * g_height; +ht = 0.07 * g_height; +wd = 1.01 * g_width; +document.write( +'<img border=0 src="slide0020_image095.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.44 * g_height; myleft = 0.47 * g_width; myheight = 0.12 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-272 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:233%;color:#F6BF69'>Low<br> </span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-272 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:233%;color:#F6BF69;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.58 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.04 * g_height; mywidth = 1.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:"-200 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;mso-line-spacing:"-200 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Gadget;font-size:167%; color:white'>>>>>PROMOTER--ATG-Exon1-Intron1-Exon2-Intron2 - etc-3'UTR >>>>></span></div> </layer></div> </layer><script> + mytop = 0.37 * g_height; myleft = 0.08 * g_width; myheight = 0.2 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.08 * g_width; +yy = 0.37 * g_height; +ht = 0.2 * g_height; +wd = 0.13 * g_width; +document.write( +'<img border=0 src="slide0020_image096.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.4 * g_height; myleft = 0.1 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> + mytop = 0.4 * g_height; myleft = 0.18 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> + mytop = 0.33 * g_height; myleft = 0.08 * g_width; myheight = 0.2 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.08 * g_width; +yy = 0.33 * g_height; +ht = 0.2 * g_height; +wd = 0.13 * g_width; +document.write( +'<img border=0 src="slide0020_image097.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.36 * g_height; myleft = 0.18 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> + mytop = 0.36 * g_height; myleft = 0.1 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> + mytop = 0.37 * g_height; myleft = 0.2 * g_width; myheight = 0.12 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;display:none'><b><br> </b></span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> + mytop = 0.27 * g_height; myleft = 0.04 * g_width; myheight = 0.21 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.04 * g_width; +yy = 0.27 * g_height; +ht = 0.21 * g_height; +wd = 0.21 * g_width; +document.write( +'<img border=0 src="slide0020_image098.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.27 * g_height; myleft = 0.05 * g_width; myheight = 0.12 * g_height; mywidth = 0.2 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D'><i>trans QTL</i></span><span style='font-size:200%;color:#E9EB5D;display:none'><br> </span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>This slide is illustrates two major types of QTLs that modulate variability in transcript-relative steady state abundance.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. cis QTLs are defined as QTLs that are closely linked to the gene whose transcript is the measured trait. For example, a polymorphism in the promoter that affects binding of a transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms in enhancers or may be in 3Õ UTR binding sites that affect message stability.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. trans QTLs map far enough away from the location of the gene that gives rise to the transcript that is being measured so that we can be fairly certain that the QTL is not in the gene itself. The most blatant type of trans QTL would be a polymorphism in a transcription factor. But in the majority of cases, the trans QTLs can be far removed in a mechanistic sense from the actual events modulating transcript abundance. That is why there are three overlapping arrows in the figure.<span style="mso-spacerun: yes"> </span>The way in which an upstream polymorphism influences a downstream difference in mRNA abundance can be indirect. Effects can:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>a.<span style="mso-spacerun: yes"> </span>cross tissue types (a polymorphic liver enzyme may affect CNS gene expression)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>b.<span style="mso-spacerun: yes"> </span>cross time (the modulator is only expressed for one day during development but has permanent effects in adults)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>c.<span style="mso-spacerun: yes"> </span>may be contingent on environmental factors (heat shock may trigger the expression of a polymorphic factor that affects mRNA abundance).</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0052.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0052.htm new file mode 100755 index 00000000..7a2e03db --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0052.htm @@ -0,0 +1,115 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jul-18-05: Discovering upstream modulatory loci"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0052.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.38 * g_height; myleft = 0.05 * g_width; myheight = 0.45 * g_height; mywidth = 0.84 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.05 * g_width; +yy = 0.38 * g_height; +ht = 0.45 * g_height; +wd = 0.84 * g_width; +document.write( +'<img border=0 src="slide0021_image099.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.08 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><span style='font-family:Verdana;font-size:64%'>Discovering upstream modulatory loci</span><span style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display: none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0.18 * g_width; myheight = 0.25 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.18 * g_width; +yy = 0.2 * g_height; +ht = 0.25 * g_height; +wd = 0.19 * g_width; +document.write( +'<img border=0 src="slide0021_image100.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.32 * g_height; myleft = 0.78 * g_width; myheight = 0.25 * g_height; mywidth = 0.19 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.78 * g_width; +yy = 0.32 * g_height; +ht = 0.25 * g_height; +wd = 0.19 * g_width; +document.write( +'<img border=0 src="slide0021_image101.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Please bring the Trait Data and Analysis window to the front and look for the Interval Mapping button. Confirm that you are back to the trait amyloid beta precursor protein.<span style="mso-spacerun: yes"> </span>If so, then just click the button.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notice that the default for:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Select Chrs (chromosomes) is ALL</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Select Mapping Scale is set to GENETIC</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Options: Permutation test YES<span style="mso-spacerun: yes"> </span>(2000 is the default number)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Options: Bootstrap test YES (2000 is the default number)</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0053.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0053.htm new file mode 100755 index 00000000..d729b467 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0053.htm @@ -0,0 +1,155 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jul-18-05: WebQTL searches for upstream controllers"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0053.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'><i>WebQTL searches for upstream controllers</i></span><span style='font-family:Verdana; font-size:73%;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.71 * g_height; myleft = 0.34 * g_width; myheight = 0.19 * g_height; mywidth = 0.45 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.18 * g_height; mywidth = 0.44 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.44 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>App maps on Chr 16 (blue </i></span></span></layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.44 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>arrow points to the orange </i></span></span></layer><script> + mytop = 0.09 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.38 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>triangle) but the best </i></span></span></layer><script> + mytop = 0.13 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.38 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>locus is on Chr 7.</i></span><span style='font-size:233%;color:#E9EB5D;mso-special-format: lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0.01 * g_width; myheight = 0.53 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.08 * g_height; +ht = 0.53 * g_height; +wd = 0.98 * g_width; +document.write( +'<img border=0 src="slide0022_image102.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.46 * g_height; myleft = 0.15 * g_width; myheight = 0.53 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.15 * g_width; +yy = 0.46 * g_height; +ht = 0.53 * g_height; +wd = 0.15 * g_width; +document.write( +'<img border=0 src="slide0022_image103.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.46 * g_height; myleft = 0.8 * g_width; myheight = 0.53 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.8 * g_width; +yy = 0.46 * g_height; +ht = 0.53 * g_height; +wd = 0.1 * g_width; +document.write( +'<img border=0 src="slide0022_image104.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.41 * g_height; myleft = 0.76 * g_width; myheight = 0.22 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.76 * g_width; +yy = 0.41 * g_height; +ht = 0.22 * g_height; +wd = 0.11 * g_width; +document.write( +'<img border=0 src="slide0022_image105.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.41 * g_height; myleft = 0.29 * g_width; myheight = 0.24 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.29 * g_width; +yy = 0.41 * g_height; +ht = 0.24 * g_height; +wd = 0.12 * g_width; +document.write( +'<img border=0 src="slide0022_image106.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>This is a major output type: a so-called full-genome interval map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The X-axis represents all 19 autosomes and the X chromosome as if they were laid end to end with short gaps between the telomere of one chromosome and the centromere of the next chromosome (mouse chromosomes only have a single long arm and the centromere represents the origin of each chromosome for numerical purpose: 0 centimorgans at almost 0 megabases). The blue labels along the bottom of the figure list a subset of the 3795 markers that were used in mapping.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The thick blue wavy line running across chromosomes summarizes the strength of association between variation in the phenotype (App expression differences) and the two genotypes of all markers and the intervals between markers (hence, interval mapping).<span style="mso-spacerun: yes"> </span>The height of the wave (blue Y-axis to the left) provides the likelihood ratio statistic (LRS). Divide by 4.61 to convert these values to LOD scores.<span style="mso-spacerun: yes"> </span>Or you can read them as a chi-square-like statistic.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The red line and the red axis to the far right provides an estimate of the effect that a QTL has on expression of App (this estimate of the so-called additive effect tends to be too high). If the red line is below the X-axis then this means that the allele inherited from C57BL/6J (B6 or B) at a particular marker is associated with higher values. If the red line is above the X-axis then the DBA/2J allele (D2 or D) is associated with higher trait values. Multiply the additive effect size by 2 to estimate the difference between the set of strains that have the B/B genotype and those that have the D/D genotype at a specific marker. For example, on distal Chr 7 the red line peaks at a value of about 0.2. That means that this region of chromosome 2 is responsible for a 0.4 unit expression difference between B/B strains and the D/D strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The yellow histogram bars: These summarize the results of a whole-genome bootstrap of the trait that is performed 1000 times. What is a bootstrap? A bootstrap provides a method to evaluate whether results are robust. If we drop out one strain, do we still get the same results? When mapping quantitative traits, each strain normally gets one equally weighted vote. But using the bootstrap procedure, we give each strain a random weighting factor of between 0 and 1.<span style="mso-spacerun: yes"> </span>We then remap the trait and find THE SINGLE BEST LRS VALUE per bootstrap. We do this 1000 times. In this example, most bootstrap results cluster on Chr 3 and Chr 7 under the LRS peaks. That is somewhat reassuring. But notice that a substantial number of bootstrap are scattered around on other chromosomes. About 30% of the bootstrap resamples have a peak on Chr 7. That is pretty good, but does makes us realize that the sample we are working with is still quite small and fragile.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The horizontal dashed lines at 10.5 and 17.3 are the likelihood ratio statistic (LRS) values associated with the suggestive and significant genome-wide probabilities that were established by permutations of phenotypes across genotypes. We shuffle randomly 2000 times and obtain a distribution of peak LRS scores to generate a null distribution. Five percent of the time, one of these permuted data sets will have a peak LRS higher than 17.3. We call that level the 0.05 significance threshold for a whole genome scan. The p = 0.67 point is the the suggestive level, and corresponds to the green dashed line.<span style="mso-spacerun: yes"> </span>These thresholds are conservative for transcripts that have expression variation that is highly heritable. The putative or suggestive QTL on Chr 3 is probably more than just suggestive.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>One other point: the mapping procedure we use is computationally very fast, but it is relatively simple. We are not looking for gene-gene interactions and we are not fitting multiple QTLs in combinations. Consider this QTL analysis a first pass that will highlight hot spots and warm spots that are worth following up on using more sophisticated models.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>CLICKABLE REGIONS:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. If you click on the Chromosome number then you will generate a new map just for that chromosome.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. If you click on the body of the map, say on the blue line, then you will generate a view on a 10 Mb window of that part of the genome from the UCSC Genome Browser web site.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. If you click on a marker symbol, then you will generate a new Trait data and Analysis window with the genotypes loaded into the window just like any other trait. More on this in Section 3.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>4. You can drag these maps off of the browser window and onto your desktop. They will be saved as PNG or PDF files. You can import them into Photoshop or other programs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>5. There is also an option at the bottom of the page to download a 2X higher resolution image of this plot for papers and presentations.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>6. You can also download the results of the analysis in a text format</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0054.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0054.htm new file mode 100755 index 00000000..64dbe68f --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0054.htm @@ -0,0 +1,113 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jul-18-05: Genetic versus Physical maps for App expression"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0054.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; 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+</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 1.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'><i>Genetic versus Physical maps for App expression</i></span><span style='font-family: Verdana;font-size:73%;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0.01 * g_width; myheight = 0.39 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.08 * g_height; +ht = 0.39 * g_height; +wd = 0.98 * g_width; +document.write( +'<img border=0 src="slide0023_image107.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.35 * g_height; myleft = 0.01 * g_width; myheight = 0.54 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.35 * g_height; +ht = 0.54 * g_height; +wd = 0.98 * g_width; +document.write( +'<img border=0 src="slide0023_image108.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.91 * g_height; myleft = 0.05 * g_width; myheight = 0.07 * g_height; mywidth = 0.95 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.95 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:117%;color:#E9EB5D'><i>The difference between genetic and physical scale is analogous to measuring the </i></span></span></layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.92 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:117%;color:#E9EB5D'><i>separation between New York and Boston in either travel hours or kilometers</i></span><span style='font-size:150%;color:#E9EB5D'><i>.</i></span><span style='font-size: 167%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The map on the top has an X-axis scale based on frequency of recombinations events between markers (B to D transitions, see slide 19 for a color-coded example). These so-called genetic maps are scaled in centimorgan (recombinations per 100 gametes). In contrast, the physical map shown below the genetic map has an X-axis scale based on DNA length measured in nucleotides or base-pairs. Notice the large difference between the two maps in the size of Chr 19 (large on the genetic scale but small on the physical scale).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Also notice the large difference in the width of the chromosome 7 QTL peak. In mice, recombinations occur with higher frequency toward the telomeric side (righ sidet) of each chromosome. As a result, genetic maps are stretched out more toward the telomere relative to a physical map. The QTL on distal Chr 7 is therefore actually more precisely mapped than might appear looking at the genetic map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The physical scale is becoming more useful than the genetic scale primarily because many other data types can be easily superimposed on a physical map. You will see more examples in the next several slides.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0055.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0055.htm new file mode 100755 index 00000000..cae5b4b9 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0055.htm @@ -0,0 +1,110 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jul-18-05: Physical map for distal chromosome 7"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0055.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Physical map for distal chromosome 7</span><span style='font-family:Verdana;font-size: 73%;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.04 * g_height; mywidth = 0.92 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-size:167%;color:#E9EB5D'>Distal Chr 7 from ~120 and 132 Mb may modulate</span><span style='font-size:167%;color:#E9EB5D'><i> App</i></span><span style='font-size:200%;color:#E9EB5D;mso-special-format: lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.93 * g_height; myleft = 0.06 * g_width; myheight = 0.03 * g_height; mywidth = 0.75 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.06 * g_width; +yy = 0.93 * g_height; +ht = 0.03 * g_height; +wd = 0.75 * g_width; +document.write( +'<img border=0 src="slide0024_image109.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0.06 * g_width; myheight = 0.75 * g_height; mywidth = 0.68 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.06 * g_width; +yy = 0.15 * g_height; +ht = 0.75 * g_height; +wd = 0.68 * g_width; +document.write( +'<img border=0 src="slide0024_image111.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Physical map of variation in App expression in brain on distal Chr 7 (a blow up of the whole-genome map on the previous slide).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Verdana size=3> You can now see that the X-axis is on a physical scale of megabases (Mb). The QTL peak is roughly between 120 and 132 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. The small irregular colored blocks and marks toward the top of the map mark the locations of genes superimposed on the physical map. Neighboring genes are offset slightly in the vertical axis for display purpose. Note one region of very high gene density from about 120 to 123 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. The orange hash marks along the X-axis represent the number of single nucleotide polymorphisms that distinguish the two parental strains (C57BL/6J and DBA/2J) from each other. We call this the SNP seismograph track (see Glossary for more details). Regions with low numbers of SNP have closely matched sequences and are less likely to contain QTLs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>4. As before, the thin red line shows the additive effect size. By convention the positive values signify the D alleles are associated with higher expression of App in this region of Chr 7 than the B alleles. The maximum effect size is about +0.20 log2 expression units per D allele. The differences been the BB and DD genotypes (BB and DD because each strain has two alleles; one per chromosome) is therefore about 2^0.4 = 1.32; or a 32% increment in DD relative to BB at this locus.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>5. If you scroll just under the Physical Map you will see text that reads ÒDISPLAY from XXX Mb TO YYY MbÉ..Ó<span style="mso-spacerun: yes"> </span>These physical maps are zoomable, a feature we will exploit to evaluate candidate genes in this QTL interval.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0056.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0056.htm new file mode 100755 index 00000000..eba3fc05 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0056.htm @@ -0,0 +1,134 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jul-18-05: Evaluating candidate genes"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0056.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.34 * g_height; myleft = 0.01 * g_width; myheight = 0.61 * g_height; mywidth = 0.97 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.34 * g_height; +ht = 0.61 * g_height; +wd = 0.97 * g_width; +document.write( +'<img border=0 src="slide0025_image112.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = -0.01 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><span style='font-family:Verdana;font-size:64%'>Evaluating candidate genes</span><span style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display: none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0.01 * g_width; myheight = 0.22 * g_height; mywidth = 0.34 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.08 * g_height; +ht = 0.22 * g_height; +wd = 0.34 * g_width; +document.write( +'<img border=0 src="slide0025_image113.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.03 * g_height; myleft = 0.69 * g_width; myheight = 0.17 * g_height; mywidth = 0.33 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.16 * g_height; mywidth = 0.31 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.31 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>Right position<br> </i></span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 0.31 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.31 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>and high </i></span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.31 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>correlation</i></span></span></layer></div> </layer></div> </layer></div> </layer><script> + mytop = 0.17 * g_height; myleft = 0.75 * g_width; myheight = 0.14 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.12 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center'><span style='font-size:267%;color:#E9EB5D'><i><span style="mso-spacerun: yes"> </span></i></span><span style='font-size:200%; color:#E9EB5D'><i>= better<br> </i></span></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>candidates</i></span></div> </layer></div> </layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4><b>Evaluating candidate genes (CHECKED BOXES) responsible for variability in APP expression:</b></font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>A large number of genes are usually in the QTL interval and are therefore POSITIONAL CANDIDATES, but they will differ greatly in their biological and bioinformatic plausibility. Assume that the QTL has been located between 119 and 131 Mb (12 Mb). There will typically be 12 to 15 genes per Mb, so we might need to evaluate several hundred positional candidates. In this particular case there are about 100 known genes in this interval. Eight of these are highlighted in the table above with check marks in the boxes to the left.<span style="mso-spacerun: yes"> </span>We need to highlight and objectively score the biologically relevant subset of all 100 positional candidate genes. We could look through gene ontologies and expression levels to help us shorten the list. An alternate way available using WebQTL is to generate a list of those genes in this interval that have transcripts that co-vary in expression with App expression. That is what the table shows.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. To replicate this table go back to the Trait Data and Analysis Form. Choose to sort correlations by POSITION and select RETURN = 500. Then scroll down the list to Chr 7 and review the subset of positional candidates that share expression with App. You should see a list similar to that shown above. Gtf3c1 is a good biological candidate and has a high covariation in expression with App.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>2. Caveat:<span style="mso-spacerun: yes"> </span>Of course, the gene or genes that control App expression may not be in this list. A protein coding difference might be the ultimate cause of variation in App transcript level and the expression covariation might be close to zero. Our list may also simply be missing the right transcript since the microarray is not truly comprehensive. Furthermore, even if the list contains the QT gene, an expression difference may only have been expressed early in development or even in another tissue such as liver. While it is important to recognize these caveats, it is equally important to devise a rational way to rank candidates given existing data. Coexpression is one of several criteria used to evaluate positional candidates. We will see others in the next slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>3. We can also assess the likelihood that candidates contain functional polymorphism in promoters and enhancers that affect their expression simply by mapping the transcripts of all candidate genes to see if they Òmap backÓ to the location of gene itself. A transcript that maps to its own location is referred to as a cis QTL. We essentially ask: Which of the the transcripts listed in the Correlation Table above (from Gtf3c1 to Zranb1) has variation in expression that maps to Chr 7 at about 120 Mb?<span style="mso-spacerun: yes"> </span>The logic of this search is that if a gene controls the level of its own expression it is also much more likely to generate other downstream effects. The Gtf3c1 transcript is a weak cis QTL with a local LRS maximum of about 7.0 (D alleles are high). That is just about sufficient to declare it to be a cis QTL. [No whole genome correction is required and a point-wise p-value of 0.05 is the appropriate test. A p-value of 0.05 is roughly equivalent to an LRS of 6.0 (LOD = 1.3).]</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0057.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0057.htm new file mode 100755 index 00000000..dcc5ede7 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0057.htm @@ -0,0 +1,115 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jul-18-05: Physical maps are zoomable"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0057.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Physical maps are zoomable</span><span style='font-family:Verdana;font-size:73%; mso-special-format:lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0.03 * g_width; myheight = 0.41 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.03 * g_width; +yy = 0.08 * g_height; +ht = 0.41 * g_height; +wd = 0.89 * g_width; +document.write( +'<img border=0 src="slide0026_image114.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.44 * g_height; myleft = 0.07 * g_width; myheight = 0.48 * g_height; mywidth = 0.42 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.07 * g_width; +yy = 0.44 * g_height; +ht = 0.48 * g_height; +wd = 0.42 * g_width; +document.write( +'<img border=0 src="slide0026_image115.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.94 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.97 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0 * g_width; +yy = 0.94 * g_height; +ht = 0.03 * g_height; +wd = 0.97 * g_width; +document.write( +'<img border=0 src="slide0026_image116.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Even higher blow-up of part of the Chr 7 physical map of variation in App expression in brain.<span style="mso-spacerun: yes"> </span>The QTL region actually extends from about 119 to 129.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. As mentioned in the previous slide another important approach to ranking candidates is based on the number of sequence variants that distinguish the parental strains. If we were sure that the sequences of the gene, its promoter, and its enhancers were identical between the strains then we could discount--but not eliminate--that gene as a candidate. The Gtf3c1 candidate almost falls into this category: of 663 known SNPs in and around this gene, only four differ between C57BL/6J and DBA/2J. Gtf3c1 is essentially identical-by-descent in these strains and is a less likely candidate. In contrast, if the two alleles of the gene have dozens of functional variants in exons, promoters, enhancers, and splice sites, then it becomes a higher priority candidate.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Of course it only takes a single critical sequence variant to generate downstream effects. The argument above is really about the prior probabilities. Where would you place your bets given the information at hand?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2.<span style="mso-spacerun: yes"> </span>If you scroll down the INTERVAL ANALYST you will find that Ctbp2 is a particularly interesting candidate that contains lots of SNPs (n = 75 and a SNP density of 0.55 SNP/Kb). Ctbp2 is also closer to our QTL peak than was Gtf3c1. Not only does Ctbp2 contain lots of SNPs but it is also is associated with a powerful cis QTL with an LRS of 24.2 (divide by 4.61 to get the equivalent LOD score of 5.25).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3.<span style="mso-spacerun: yes"> </span>At this high magnification, individual genes are distinct. They are color coded by their density of SNPs. Bright orange represents those genes that have a high SNP density (C57BL/6J versus DBA/2J), black represents genes with low SNP density. Roll the cursor over a gene block and its name will pop up, along with information on exon number.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>4.<span style="mso-spacerun: yes"> </span>Beneath the physical map you will find an INTERVAL ANALYST table that lists information on known genes in the region on which you have zoomed the Physical Map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>5.<span style="mso-spacerun: yes"> </span>As always: error-checking is important. Some genes may be missing from the Interval Analyst (recent additions or errors of omission). In this case the Zranb1 gene that is located just proximal to Ctbp2 is not listed in the INTERVAL ANALYST. Double-check the interval using the Genome Browser links (blue and beige horizontal bars) at the top of the PHYSICAL MAP.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0058.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0058.htm new file mode 100755 index 00000000..47e08c87 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0058.htm @@ -0,0 +1,167 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jul-18-05: Evaluating Ctbp2 as a candidate QTL for App"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0058.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Evaluating </span><span style='font-family:Verdana;font-size:64%'><i>Ctbp2</i></span><span style='font-family:Verdana;font-size:64%'> as a candidate QTL for </span><span style='font-family:Verdana;font-size:64%'><i>App</i></span><span style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display: none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.94 * g_height; myleft = 0.03 * g_width; myheight = 0.04 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.03 * g_width; +yy = 0.94 * g_height; +ht = 0.04 * g_height; +wd = 0.96 * g_width; +document.write( +'<img border=0 src="slide0027_image118.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.03 * g_width; myheight = 0.4 * g_height; mywidth = 0.48 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.03 * g_width; +yy = 0.07 * g_height; +ht = 0.4 * g_height; +wd = 0.48 * g_width; +document.write( +'<img border=0 src="slide0027_image119.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.52 * g_height; myleft = 0.55 * g_width; myheight = 0.37 * g_height; mywidth = 0.35 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.33 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>This is</span><span style='font-size:233%;color:#E9EB5D'><i> the </i></span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.34 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2 </i></span><span style='font-size:233%;color:#E9EB5D'>cis QTL, </span></span></layer><script> + mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.35 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>but is detected </span></span></layer><script> + mytop = 0.18 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.33 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>only in the </span></span></layer><script> + mytop = 0.25 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.35 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>Rosen striatum </span></span></layer><script> + mytop = 0.31 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.33 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>data set.</span><span style='font-size:233%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0.56 * g_width; myheight = 0.12 * g_height; mywidth = 0.48 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.45 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>This is</span><span style='font-size:233%;color:#E9EB5D'><i> the App QTL </i></span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.48 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>in the INIA data set. </span><span style='font-size:233%;color:#E9EB5D;mso-special-format: lastCR;display:none'><i><br> </i></span></span></layer></div> </layer><script> + mytop = 0.39 * g_height; myleft = 0.03 * g_width; myheight = 0.53 * g_height; mywidth = 0.48 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.03 * g_width; +yy = 0.39 * g_height; +ht = 0.53 * g_height; +wd = 0.48 * g_width; +document.write( +'<img border=0 src="slide0027_image120.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.35 * g_width; myheight = 0.72 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.35 * g_width; +yy = 0.1 * g_height; +ht = 0.72 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0027_image121.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.31 * g_width; myheight = 0.72 * g_height; mywidth = 0 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.31 * g_width; +yy = 0.1 * g_height; +ht = 0.72 * g_height; +wd = 0 * g_width; +document.write( +'<img border=0 src="slide0027_image122.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>This slide illustrates one reason why Ctbp2 should be considered a high priority positional candidate gene that may modulate the expression level of App.<span style="mso-spacerun: yes"> </span>Ctbp2 is a strong cis QTL in some brain regions (here the data are taken from the striatum).<span style="mso-spacerun: yes"> </span>If Ctbp2 contains variants that modulate its own expression then these expression differencess may produce many downstream effects. Of course, we now want to know much more about the known biology of Ctbp2. What kind of gene is it? To begin to answer that question we can use a number of resources listed in the LINKS page.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Verdana size=3> The App QTL is bimodal. Perhaps there are actually two causal factors in this region--one close to 123 Mb and the other close to 127 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. The precision of QTL mapping depends on several factors, including the effect size and interactions among QTLs modulating a trait, the number of genetic individuals that are studied, and the distribution of recombinations in the study population.<span style="mso-spacerun: yes"> </span>In the case above, the QTL(s) are likely to be confined to the interval from 120 to 132 Mb. The bootstrap test (yellow bars shown in some of the previous slides) can be usual for estimating the consiistency of QTL peaks.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0059.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0059.htm new file mode 100755 index 00000000..5ba9ff5c --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0059.htm @@ -0,0 +1,104 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jul-18-05: Evaluating Ctbp2 using other resources"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0059.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Evaluating </span><span style='font-family:Verdana;font-size:64%'><i>Ctbp2</i></span><span style='font-family:Verdana;font-size:64%'> using other resources</span><span style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display: none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.01 * g_width; myheight = 0.53 * g_height; mywidth = 0.48 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.1 * g_height; +ht = 0.53 * g_height; +wd = 0.48 * g_width; +document.write( +'<img border=0 src="slide0028_image123.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.4 * g_height; myleft = 0.19 * g_width; myheight = 0.54 * g_height; mywidth = 0.78 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.19 * g_width; +yy = 0.4 * g_height; +ht = 0.54 * g_height; +wd = 0.78 * g_width; +document.write( +'<img border=0 src="slide0028_image124.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Ctbp2 should also be considered a high priority biological candidate gene responsible for modulating App expression levels. The<span style="mso-spacerun: yes"> </span>C-terminal binding protein 2 is a transcriptional co-repressor also known as Ribeye.</font><font face=Times-Roman size=3> The gene produces two transcripts encoding distinct proteins. The short form is a transcriptional repressor that binds a Pro-X-Asp-Leu-Ser peptide motif common to adenoviral oncoprotein E1a and a related motif in BKLF. This short form also interacts<span style="mso-spacerun: yes"> </span>with several transcription factors including EVI1, ZFPM1, and<span style="mso-spacerun: yes"> </span>ZFHX1A (aka TCF8, deltaEF1). The longer isoform is a major component of specialized synapses in photoreceptors. Both proteins contain a NAD+ binding domain similar to NAD+-dependent 2-hydroxyacid dehydrogenases.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. To find out more about CTBP2 protein and the Ctbp2 gene, link to iHOP at http://www.pdg.cnb.uam.es/UniPub/iHOP/ and type in CTBP2</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Try Arrowsmith at http://arrowsmith.psych.uic.edu/cgi-test/arrowsmith_uic/pubsmith.cgi</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. Both APP and CTBP2 are involved in oxidoreducatase activity or Notch signalling. To estabilish this common gene ontology visit NCBI<span style="mso-spacerun: yes"> </span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene<span style="mso-spacerun: yes"> </span>and enter each gene symbol.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. You can get intersting hints regarding Ctbp2 expression partners by examining the genetic correlations between Ctbp2 probe set 1422887_a_at and all other transcripts on the M430 Affymetrix array. Use the Striatum data set because we already know from previous work (the previous slide) that this gene is a cis QTL.<span style="mso-spacerun: yes"> </span>You should be able to show that Ctbp2 and Notch3 have antagonistic expression patterns in striatum. The negative genetic correlation with E2f4 is even stronger. The transcript also has a high positive genetic correlation with Rdh14. Of particualr interest with respect to APP protein processing, Ctbp2 covaries positiviely with Bace2 (the transcript of the beta site APP-cleaving enzyme 2).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0060.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0060.htm new file mode 100755 index 00000000..2f1c5b7b --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0060.htm @@ -0,0 +1,139 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Jul-18-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0060.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0'><span style='mso-special-format:nobullet;display: none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Summary of Part 2:</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.09 * g_height; myleft = 0.08 * g_width; myheight = 0.37 * g_height; mywidth = 1.02 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.87 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.84 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.96%;font-family:Arial'>1.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Covered the basics of QTL analysis and mapping.<br> </span></span></layer></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.95 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.92 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.71%;font-family:Arial'>2.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Reviewed difference between genetic and physical maps.<br> </span></span></layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.15 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.95 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.62%;font-family:Arial'>3.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Discussed interpreting features of QTL maps including the </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>LRS function, the additive effect function, the bootstrap bars, </span></span></layer><script> + mytop = 0.1 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.84 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>and the permutation thresholds.<br> </span></span></layer></div> </layer><script> + mytop = 0.26 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.02 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.51%;font-family:Arial'>4.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Illustrated technics to generate a list of positional candidates.<br> </span></span></layer></div> </layer><script> + mytop = 0.31 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.97 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.65%;font-family:Arial'>5.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Discussed some factors used to evaluate candidate genes.</span></span></layer></div> </layer></div> </layer><script> + mytop = 0.58 * g_height; myleft = 0.05 * g_width; myheight = 0.26 * g_height; mywidth = 1.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>What does a QTL signify? A good QTL is a claim that a particular </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>chromosomal region contains a causal source of variation in the </span></span></layer><script> + mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>phenotype. The importance of this hypothesis depends on the </span></span></layer><script> + mytop = 0.15 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.92 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>quality and relevance of the phenotype and the statistical </span></span></layer><script> + mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>strength of the QTL. As usual, test and be skeptical.</span></span></layer></div> </layer></div> </LAYER> +<script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0061.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0061.htm new file mode 100755 index 00000000..a2816092 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0061.htm @@ -0,0 +1,112 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jul-18-05: Test Questions"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0061.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; 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+</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Test Questions</span><span style='font-family:Verdana;font-size:73%;mso-special-format: lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.11 * g_height; myleft = 0.04 * g_width; myheight = 0.06 * g_height; mywidth = 1.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-size:233%;color:#E9EB5D'>1. Evaluate candidates for the Chr 3 </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span style='font-size:233%;color:#E9EB5D'> QTL.</span><span style='font-size:233%; color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </layer><script> + mytop = 0.24 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>2. Do </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span style='font-size: 233%;color:#E9EB5D'> and </span><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span style='font-size:233%;color:#E9EB5D'> expression share any </span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>other QTLs beside that on Chr 7?</span><span style='font-size:233%;color:#E9EB5D; mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer><script> + mytop = 0.45 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.02 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>3. Can you exploit literature mining tools to </span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>find strong relation between </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span style='font-size:233%;color:#E9EB5D'> and </span><span style='font-size:233%; color:#E9EB5D'><i>Ctbp2</i></span><span style='font-size:233%;color:#E9EB5D'>? </span><span style='font-size:233%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer><script> + mytop = 0.66 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 1.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>4. Why might the cis QTL for </span><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span style='font-size:233%;color:#E9EB5D'> expression </span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>only be detected in the striatum data set?</span><span style='font-size:233%; color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </LAYER> +<script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0062.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0062.htm new file mode 100755 index 00000000..6b671799 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0062.htm @@ -0,0 +1,109 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Jul-18-05: Contact for comments and improvements:"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0062.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.02 * g_height; myleft = 0.02 * g_width; myheight = 0.09 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 0.92 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><span style='font-size:73%'><i>Contact for comments and improvements:</i></span><span style='font-size:82%;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0.06 * g_width; myheight = 0.24 * g_height; mywidth = 0.9 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.24 * g_height; mywidth = 0.87 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.87 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:82%'>rwilliam@nb.utmem.edu<br> </span></span></layer><script> + mytop = 0.08 * g_height; myleft = 0.04 * g_width; myheight = 0.07 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:82%'><br> </span></span></layer><script> + mytop = 0.16 * g_height; myleft = 0.04 * g_width; myheight = 0.07 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:82%;mso-special-format:lastCR; display:none'><br> </span></span></layer></div> </layer></div> </layer><script> + mytop = 0.27 * g_height; myleft = 0.09 * g_width; myheight = 0.07 * g_height; mywidth = 0.5 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:300%; color:#E9EB5D'>kmanly@utmem.edu</span></div> </layer><script> + mytop = 0.83 * g_height; myleft = 0.04 * g_width; myheight = 0.1 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'>The </span><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'><i>App</i></span><span style='font-family:"Gill Sans"; font-size:200%;color:#E9EB5D'> findings reviewed in this presentation are part of an </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'>ongoing study of R. 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content=NoIndex> <link rel=Stylesheet href="master03_stylesheet.css"> <script language=JavaScript src=script.js></script> +<script> +<!-- + parent.location.href=document.all.item("Main-File").href +//--> +</script> + </head> <body> <div class=O style='text-align:right;position:absolute;top:.53%;left:58.01%; width:40.79%;height:2.12%'><span style='color:black'><b>Memphis Microarray 2003</b></span></div> <div class=O style='position:absolute;top:97.52%;left:1.32%;width:42.64%; height:2.12%'><span style='color:black'><b>June 11, 2003, Rob Williams</b></span></div> <div class=O style='text-align:right;position:absolute;top:97.52%;left:58.01%; width:40.79%;height:2.12%'><span style='color:black;mso-field-code:meta16'><b>Ü#Ý</b></span><span style='color:black;mso-special-format:lastCR'><b><br> </b></span></div> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/master03.htm 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b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline.gif Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_collapse.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_collapse.gif new file mode 100755 index 00000000..4c804d69 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_collapse.gif Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_collapsed.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_collapsed.htm new file mode 100755 index 00000000..5da9503b --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_collapsed.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Robots content=NoIndex> <style> <!--a {text-decoration: none;}--> </style> </head> <body bgcolor=black text=white link=white vlink=white alink=white onload=" parent.base.highlite();" onresize="self.location.reload();"> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID1 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p1" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('1')" id=AREF>GeneNetwork and WebQTL:</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID2 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p2" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('2')" id=AREF>Slide 2</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID3 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p3" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('3')" id=AREF>Slide 3</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID4 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p4" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('4')" id=AREF><font face="Gill Sans">Search results</font></a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID5 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p5" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('5')" id=AREF>"First page of data:"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID6 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p6" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('6')" id=AREF>"Data sources:"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID7 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p7" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('7')" id=AREF>"Expression estimates for App on..."</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID8 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p8" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('8')" id=AREF>"Critiquing the App data the..."</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID9 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p9" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('9')" id=AREF>"App expression after windsorizing"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID10 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p10" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('10')" id=AREF>"Discovering shared expression patterns"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID11 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p11" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('11')" id=AREF>"Transcript neighborhoods"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID12 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p12" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('12')" id=AREF>"App and Atcay transcript scatterplot"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID13 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p13" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('13')" id=AREF>"App transcript and eight of..."</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID14 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p14" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('14')" id=AREF>App transcript coexpression neighborhood</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID15 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p15" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('15')" id=AREF>"Correlations of App with classical..."</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID16 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p16" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('16')" id=AREF>"Network Graph of App with..."</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID17 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p17" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('17')" id=AREF>"Summary of Part 1:"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID18 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p18" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('18')" id=AREF>Contact for comments and improvements:</a></b></font></td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_expand.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_expand.gif new file mode 100755 index 00000000..c8c72b13 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_expand.gif Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_expanded.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_expanded.htm new file mode 100755 index 00000000..a45e9c0c --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_expanded.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Robots content=NoIndex> <style> <!--a {text-decoration: none;}--> </style> </head> <body bgcolor=black text=white link=white vlink=white alink=white onload=" parent.base.highlite();" onresize="self.location.reload();"> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID1 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p1" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('1')" id=AREF>GeneNetwork and WebQTL:</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Part 1: How to study expression variation and covariation (slides 2–16)</font></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Part 2. Discovering upstream modulators (slides 17–30)</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID2 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p2" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('2')" id=AREF>Slide 2</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID3 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p3" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('3')" id=AREF>Slide 3</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID4 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p4" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('4')" id=AREF><font face="Gill Sans">Search results</font></a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID5 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p5" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('5')" id=AREF>"First page of data:"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>First page of data: The Trait Data and Analysis Form</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID6 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p6" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('6')" id=AREF>"Data sources:"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Data sources: Metadata for each resource</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID7 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p7" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('7')" id=AREF>"Expression estimates for App on..."</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Expression estimates for App on the Trait Data form</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID8 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p8" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('8')" id=AREF>"Critiquing the App data the..."</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Critiquing the App data the Trait Data</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID9 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p9" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('9')" id=AREF>"App expression after windsorizing"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>App expression after windsorizing</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID10 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p10" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('10')" id=AREF>"Discovering shared expression patterns"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Discovering shared expression patterns</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID11 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p11" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('11')" id=AREF>"Transcript neighborhoods"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Transcript neighborhoods</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID12 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p12" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('12')" id=AREF>"App and Atcay transcript scatterplot"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>App and Atcay transcript scatterplot</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID13 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p13" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('13')" id=AREF>"App transcript and eight of..."</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>App transcript and eight of its neighbors</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID14 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p14" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('14')" id=AREF>App transcript coexpression neighborhood</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID15 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p15" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('15')" id=AREF>"Correlations of App with classical..."</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Correlations of App with classical traits</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID16 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p16" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('16')" id=AREF>"Network Graph of App with..."</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Network Graph of App with classical traits</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID17 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p17" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('17')" id=AREF>"Summary of Part 1:"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Summary of Part 1:</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID18 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p18" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('18')" id=AREF>Contact for comments and improvements:</a></b></font></td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_navigation_bar.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_navigation_bar.htm new file mode 100755 index 00000000..f47a3707 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_navigation_bar.htm @@ -0,0 +1,37 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script><script language=JavaScript><!-- + +function restore() { +if( navigator.platform != "MacPPC" ) + self.location.reload(); 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+ } +}//--> +</script> </head> <body background=navbg.gif topmargin=1 onresize="restore()" scroll="no" > <script language=JavaScript><!-- +writebody(); +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/prev_active.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/prev_active.gif new file mode 100755 index 00000000..004a872f --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/prev_active.gif Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/prev_disabled.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/prev_disabled.gif new file mode 100755 index 00000000..8a467185 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/prev_disabled.gif Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/script.js b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/script.js new file mode 100755 index 00000000..7c9fb703 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/script.js @@ -0,0 +1,1351 @@ +var CtxAlwaysOn = false; +function LoadSld( slideId ) +{ + if( !g_supportsPPTHTML ) return + if( slideId ) + parent.base.SldUpdated(slideId) + g_origSz=parseInt(SlideObj.style.fontSize) + g_origH=SlideObj.style.posHeight + g_origW=SlideObj.style.posWidth + g_scaleHyperlinks=(document.all.tags("AREA").length>0) + if ( IsWin("PPTSld") && !parent.IsFullScrMode() ) + parent.base.highlite(); + if( g_scaleHyperlinks ) + InitHLinkArray() + if( g_scaleInFrame||(IsWin("PPTSld") && parent.IsFullScrMode() ) ) + document.body.scroll="no" + _RSW() + if( IsWin("PPTSld") && (parent.IsFullScrMode() || CtxAlwaysOn ) ) { + document.oncontextmenu=parent._CM; + self.focus(); + + } +} +function MakeSldVis( fTrans ) +{ + fTrans=fTrans && g_showAnimation + if( fTrans ) + { + if( g_bgSound ) { + idx=g_bgSound.indexOf(","); + pptSound.src=g_bgSound.substr( 0, idx ); + pptSound.loop= -(parseInt(g_bgSound.substr(idx+1))); + } + SlideObj.filters.revealtrans.Apply() + } + SlideObj.style.visibility="visible" + if( fTrans ) + SlideObj.filters.revealtrans.Play() +} +function MakeNotesVis() +{ + if( !IsNts() ) return false + SlideObj.style.display="none" + nObj = document.all.item("NotesObj") + parent.SetHasNts(0) + if( nObj ) { + nObj.style.display="" + parent.SetHasNts(1) + } + return 1 +} +function Redirect( frmId,sId ) +{ + var str=document.location.hash,idx=str.indexOf('#') + if(idx>=0) str=str.substr(1); + if( window.name != frmId && ( sId != str) ) { + obj = document.all.item("Main-File") + window.location.href=obj.href+"#"+sId + return 1 + } + return 0 +} +function HideMenu() { if( frames["PPTSld"] && PPTSld.document.all.item("ctxtmenu") && PPTSld.ctxtmenu.style.display!="none" ) { PPTSld.ctxtmenu.style.display='none'; return true } return false } +function IsWin( name ) { return window.name == name } +function IsNts() { return IsWin("PPTNts") } +function IsSldOrNts() { return( IsWin("PPTSld")||IsWin("PPTNts") ) } +function SupportsPPTAnimation() { return( navigator.platform == "Win32" && navigator.appVersion.indexOf("Windows")>0 ) } +function SupportsPPTHTML() +{ + var appVer=navigator.appVersion, msie=appVer.indexOf( "MSIE " ), inex = appVer.indexOf( "Internet Explorer " ), ver=0 + if( msie >= 0 ) + ver=parseFloat( appVer.substring( msie+5, appVer.indexOf(";",msie) ) ) + else if( inex >= 0 ) + ver=parseFloat( appVer.substring( inex+18, appVer.indexOf(";",inex) ) ) + else + ver=parseInt(appVer) + + return( ver >= 4 ) +} +var MHTMLPrefix = CalculateMHTMLPrefix(); +function CalculateMHTMLPrefix() +{ + if ( document.location.protocol == 'mhtml:') { + href=new String(document.location.href) + Start=href.indexOf('!')+1 + End=href.lastIndexOf('/')+1 + if (End < Start) + return href.substring(0, Start) + else + return href.substring(0, End) + } + return ''; +} + +function LoadNavSld(slideId) { +playList(); +parent.createCM(); + if( !g_supportsPPTHTML ) return + if( IsWin("PPTSld") && slideId ) + parent.base.SldUpdated(slideId) + self.focus(); + +} +var hasNarration = false; +function _RSW() +{ + if( !g_supportsPPTHTML || IsNts() || + ( !g_scaleInFrame && (( window.name != "PPTSld" ) ) ) ) + return + + cltWidth=document.body.clientWidth + cltHeight=document.body.clientHeight + factor=(1.0*cltWidth)/g_origW + if( cltHeight < g_origH*factor ) + factor=(1.0*cltHeight)/g_origH + + newSize = g_origSz * factor + if( newSize < 1 ) newSize=1 + + s=SlideObj.style + s.fontSize=newSize+"px" + s.posWidth=g_origW*factor + s.posHeight=g_origH*factor + s.posLeft=(cltWidth-s.posWidth)/2 + s.posTop=(cltHeight-s.posHeight)/2 + + if ( hasNarration ) { + obj = document.all.NSPlay.style; + mySld = document.all.SlideObj.style; + obj.position = 'absolute'; + obj.posTop = mySld.posTop + mySld.posHeight - 20; + obj.posLeft = mySld.posLeft + mySld.posWidth - 20; + } + if( g_scaleHyperlinks ) + ScaleHyperlinks( factor ); +} +function IsMac() { + return (window.navigator.platform.indexOf("Mac") >= 0 ); +} + +function HitOK( evt ) { + //Nav Only function + return (evt.which == 1 || (IsMac() && evt.which == 3) ); +} +function _KPH(event) +{ + + if ( parent.base.msie < 0 ) { + + if ( ( (event.target.name && event.target.name == "hasMap" ) || (event.target.href && event.target.href != "") ) && parent.g_docTable[0].type != "jpeg" && HitOK( event ) ) { + return; /* to make hyperlinks in fullscreen mode traversable */ + } + if( IsContextMenu() ) + return parent.KPH(event); + if ( parent.IsFullScrMode() && event.which == 27 ) + parent.base.CloseFullScreen(); + else if ( parent.base.IsFullScrMode() && ( (!IsMac() && event.which == 3) || ( IsMac() && (event.modifiers & Event.CONTROL_MASK) && event.which == 1 ) ) ) + return parent.KPH(event); + else if( (event.which == 32) || (event.which == 13) || HitOK( event ) ) { + if( window.name == "PPTSld" ) + parent.PPTSld.DocumentOnClick(); + else + parent.M_GoNextSld(); + } + else if ( parent.IsFullScrMode() && ((event.which == 78) || (event.which == 110) || (event.which == 29) || (event.which == 31) || (event.which == 12)) ) + parent.M_GoNextSld(); + else if ( parent.IsFullScrMode() && ( (event.which == 80) || (event.which == 112) || (event.which == 30) || (event.which == 28) || (event.which == 11) || (event.which == 8)) ) + parent.M_GoPrevSld(); + + return; + } + + if( IsNts() ) return; + + if(parent.IsFullScrMode() && event.keyCode == 27 && !parent.HideMenu() ) + parent.base.CloseFullScreen(); + else if( (event.keyCode == 32) || (event.keyCode == 13) ) + { + if( window.name == "PPTSld" ) + parent.PPTSld.DocumentOnClick(); + else + parent.M_GoNextSld(); + } + else if ( parent.IsFullScrMode() && ((event.keyCode == 78) || (event.keyCode == 110)) ) + parent.M_GoNextSld(); + else if ( parent.IsFullScrMode() && ((event.keyCode == 80) || (event.keyCode == 112)) ) + parent.M_GoPrevSld(); +} + +function DocumentOnClick(event) +{ + if ( g_doAdvOnClick && !parent.IsFullScrMode() ) { + parent.base.TP_GoToNextSld(); + return; + } + + if ( parent.base.msie < 0 ) + { + if( ( g_allowAdvOnClick && parent.IsFullScrMode() ) || g_doAdvOnClick || + (event && ( (event.which == 32) || (event.which == 13) ) ) ) + parent.M_GoNextSld(); + return; + } + if( IsNts() || (parent.IsFullScrMode() && parent.HideMenu() ) ) return; + if( ( g_allowAdvOnClick && parent.IsFullScrMode() ) || g_doAdvOnClick || + (event && ( (event.keyCode==32) || (event.keyCode == 13) ) ) ) + parent.M_GoNextSld(); +} + + +var g_supportsPPTHTML = SupportsPPTHTML(), g_scaleInFrame = true, gId="", g_bgSound="", + g_scaleHyperlinks = false, g_allowAdvOnClick = true, g_showInBrowser = false, g_doAdvOnClick = false; + + var g_showAnimation = 0; +var g_hasTrans = false, g_autoTrans = false, g_transSecs = 0; +var g_animManager = null; + +var ENDSHOW_MESG="End of slide show, click to exit.", SCREEN_MODE="Frames", gIsEndShow=0, NUM_VIS_SLDS=18, SCRIPT_HREF="script.js", FULLSCR_HREF="fullscreen.htm"; +var gCurSld = gPrevSld = 1, g_offset = 0, gNtsOpen = gHasNts = gOtlTxtExp = gNarrationPaused = false, gOtlOpen = true +window.gPPTHTML=SupportsPPTHTML() +var g_hideNav = 0; +function UpdNtsPane(){ PPTNts.location.replace( MHTMLPrefix+GetHrefObj( gCurSld ).mNtsHref ) } +function UpdNavPane( sldIndex ){ if(gNavLoaded) PPTNav.UpdNav() } +function UpdOtNavPane(){ if(gOtlNavLoaded) PPTOtlNav.UpdOtlNav() } +function UpdOtlPane(){ if(gOtlLoaded) PPTOtl.UpdOtl() } +function SetHasNts( fVal ) +{ + if( gHasNts != fVal ) { + gHasNts=fVal + UpdNavPane() + } +} + +function ToggleVNarration() +{ + if ( base.msie < 0 ) { + PPTSld.ToggleSound( false, PPTSld.document.NSPlay ); + return; + } + + rObj=PPTSld.document.all("NSPlay") + if( rObj ) { + if( gNarrationPaused ) + rObj.Play() + else + rObj.Pause() + + gNarrationPaused=!gNarrationPaused + } +} + +function PrevSldViewed(){ GoToSld( GetHrefObj(gPrevSld).mSldHref ) } +function HasPrevSld() { return ( gIsEndShow || ( g_currentSlide != 1 && GetHrefObj( g_currentSlide-1 ).mVis == 1 )||( GetCurrentSlideNum() > 1 ) ) } +function HasNextSld() { return (GetCurrentSlideNum() != GetNumSlides()) } +function StartEndShow() +{ +// g_hideNav = 1; +// PPTNav.location.reload(); + if( PPTSld.event ) PPTSld.event.cancelBubble=true + + doc=PPTSld.document + doc.open() + doc.writeln('<html><head><script > /*defer>*/ g_ctxmenu = 0; ' + + 'if( parent.base.msie < 0 ) { document.captureEvents(Event.KEYPRESS); document.captureEvents(Event.MOUSEDOWN); document.onkeypress = _KPH; document.onmousedown = _KPH; } ' + + 'function DocumentOnClick(event) { return _KPH(event); } function IsContextMenu() { return (g_ctxmenu ==1); } ' + + 'function _KPH(event)' + + '{ ' + + 'if ( parent.base.msie < 0 && (parent.IsFullScrMode() ) && event ) { if ( (!parent.IsMac() && event.which == 3) || ( parent.IsMac() && (event.modifiers & Event.CONTROL_MASK) && event.which == 1 ) ) { return parent.KPH(event); } ' + + ' else if (event.which == 27 || event.which == 32 || event.which == 13 || parent.HitOK( event ) || (event.which == 78) || (event.which == 110) || (event.which == 29) || (event.which == 31) || (event.which == 12) ) { if ( IsContextMenu() ) { return parent.KPH(event); } parent.base.CloseFullScreen(); return; } ' + + ' else if ( (event.which == 80) || (event.which == 112) || (event.which == 30) || (event.which == 28) || (event.which == 11) || (event.which == 8) ) { parent.M_GoPrevSld(); } } ' + + 'if( parent.HideMenu() ) return; if( (parent.IsFullScrMode() ) && event) { if ( (event.keyCode==27 || event.keyCode == 13 || event.keyCode==32 || event.type=="click" ) || (event.keyCode == 78) || (event.keyCode == 110) ) { parent.base.CloseFullScreen(); }' + + ' else if ( (event.keyCode == 80) || (event.keyCode == 112) ) { parent.M_GoPrevSld(); } } } function Unload() { parent.gIsEndShow=0; } function SetupEndShow() { if ( !parent.IsFullScrMode() ) { return; } else { parent.PPTNav.location.reload(); } parent.gIsEndShow=1; if ( parent.g_docTable[0].type != "jpeg" ) { if ( parent.base.msie < 0 ) {parent.createCM(); } document.oncontextmenu=parent._CM; } }</script></head><body scroll=\"no\" onclick=\"DocumentOnClick(event)\" onkeypress=\"_KPH(event)\" bgcolor=\"black\" onload=\"SetupEndShow()\" onunload=\"Unload()\"><center><p><font face=Tahoma color=white size=2><br><b>' + ENDSHOW_MESG + '</b></font></p></center></body></html>') + doc.close() +} +function SetSldVisited(){ gDocTable[gCurSld-1].mVisited=true } +function IsSldVisited(){ return gDocTable[gCurSld-1].mVisited } +function hrefList( sldHref, visible, sldIdx ) +{ + this.mSldHref= this.mNtsHref = sldHref + this.mSldIdx = sldIdx + this.mOrigVis= this.mVis = visible + this.mVisited= false +} +var gDocTable = new Array( + new hrefList("slide0001.htm", 1, 1), + new hrefList("slide0002.htm", 1, 2), + new hrefList("slide0003.htm", 1, 3), + new hrefList("slide0004.htm", 1, 4), + new hrefList("slide0005.htm", 1, 5), + new hrefList("slide0006.htm", 1, 6), + new hrefList("slide0007.htm", 1, 7), + new hrefList("slide0008.htm", 1, 8), + new hrefList("slide0009.htm", 1, 9), + new hrefList("slide0010.htm", 1, 10), + new hrefList("slide0011.htm", 1, 11), + new hrefList("slide0012.htm", 1, 12), + new hrefList("slide0013.htm", 1, 13), + new hrefList("slide0014.htm", 1, 14), + new hrefList("slide0015.htm", 1, 15), + new hrefList("slide0016.htm", 1, 16), + new hrefList("slide0017.htm", 1, 17), + new hrefList("slide0018.htm", 1, 18) +); + +function ImgBtn( oId,bId,w,action ) +{ + var t=this + t.Perform = _IBP + t.SetActive = _IBSetA + t.SetInactive= _IBSetI + t.SetPressed = _IBSetP + t.SetDisabled= _IBSetD + t.Enabled = _IBSetE + t.ChangeIcon = null + t.UserAction = action + t.ChgState = _IBUI + t.mObjId = oId + t.mBorderId= bId + t.mWidth = w + t.mIsOn = t.mCurState = 0 +} +function _IBSetA() +{ + if( this.mIsOn ) { + obj=this.ChgState( gHiliteClr,gShadowClr,2 ) + obj.style.posTop=0 + } +} +function _IBSetI() +{ + if( this.mIsOn ) { + obj=this.ChgState( gFaceClr,gFaceClr,1 ) + obj.style.posTop=0 + } +} +function _IBSetP() +{ + if( this.mIsOn ) { + obj=this.ChgState( gShadowClr,gHiliteClr,2 ) + obj.style.posLeft+=1; obj.style.posTop+=1 + } +} +function _IBSetD() +{ + obj=this.ChgState( gFaceClr,gFaceClr,0 ) + obj.style.posTop=0 +} +function _IBSetE( state ) +{ + var t=this + GetObj( t.mBorderId ).style.visibility="visible" + if( state != t.mIsOn ) { + t.mIsOn=state + if( state ) + t.SetInactive() + else + t.SetDisabled() + } +} +function _IBP() +{ + var t=this + if( t.mIsOn ) { + if( t.UserAction != null ) + t.UserAction() + if( t.ChangeIcon ) { + obj=GetObj(t.mObjId) + if( t.ChangeIcon() ) + obj.style.posLeft=obj.style.posLeft+(t.mCurState-4)*t.mWidth + else + obj.style.posLeft=obj.style.posLeft+(t.mCurState-0)*t.mWidth + } + t.SetActive() + } +} +function _IBUI( clr1,clr2,nextState ) +{ + var t=this + SetBorder( GetObj( t.mBorderId ),clr1,clr2 ) + obj=GetObj( t.mObjId ) + obj.style.posLeft=obj.style.posLeft+(t.mCurState-nextState)*t.mWidth-obj.style.posTop + t.mCurState=nextState + return obj +} +function TxtBtn( oId,oeId,action,chkState ) +{ + var t=this + t.Perform = _TBP + t.SetActive = _TBSetA + t.SetInactive= _TBSetI + t.SetPressed = _TBSetP + t.SetDisabled= _TBSetD + t.SetEnabled = _TBSetE + t.GetState = chkState + t.UserAction = action + t.ChgState = _TBUI + t.mObjId = oId + t.m_elementsId= oeId + t.mIsOn = 1 +} +function _TBSetA() +{ + var t=this + if( t.mIsOn && !t.GetState() ) + t.ChgState( gHiliteClr,gShadowClr,0,0 ) +} +function _TBSetI() +{ + var t=this + if( t.mIsOn && !t.GetState() ) + t.ChgState( gFaceClr,gFaceClr,0,0 ) +} +function _TBSetP() +{ + if( this.mIsOn ) + this.ChgState( gShadowClr,gHiliteClr,1,1 ) +} +function _TBSetD() +{ + this.ChgState( gFaceClr,gFaceClr,0,0 ) + this.mIsOn = 0 +} +function _TBSetE() +{ + var t=this + if( !t.GetState() ) + t.ChgState( gFaceClr,gFaceClr,0,0 ) + else + t.ChgState( gShadowClr,gHiliteClr,1,1 ) + t.mIsOn = 1 +} +function _TBP() +{ + var t=this + if( t.mIsOn ) { + if( t.UserAction != null ) + t.UserAction() + if( t.GetState() ) + t.SetPressed() + else + t.SetActive() + } +} +function _TBUI( clr1,clr2,lOffset,tOffset ) +{ + SetBorder( GetObj( this.mObjId ),clr1,clr2 ) + Offset( GetObj( this.m_elementsId ),lOffset,tOffset ) +} +function GetObj( objId ){ return document.all.item( objId ) } +function Offset( obj, top, left ){ obj.style.top=top; obj.style.left=left } +function SetBorder( obj, upperLeft, lowerRight ) +{ + s=obj.style; + s.borderStyle = "solid" + s.borderWidth = 1 + s.borderLeftColor = s.borderTopColor = upperLeft + s.borderBottomColor= s.borderRightColor = lowerRight +} +function GetBtnObj(){ return gBtnArr[window.event.srcElement.id] } +function BtnOnOver(){ b=GetBtnObj(); if( b != null ) b.SetActive() } +function BtnOnDown(){ b=GetBtnObj(); if( b != null ) b.SetPressed() } +function BtnOnOut(){ b=GetBtnObj(); if( b != null ) b.SetInactive() } +function BtnOnUp() +{ + b=GetBtnObj() + if( b != null ) + b.Perform() + else + Upd() +} +function GetNtsState(){ return parent.gNtsOpen } +function GetOtlState(){ return parent.gOtlOpen } +function GetOtlTxtState(){ return parent.gOtlTxtExp } +function NtsBtnSetFlag( fVal ) +{ + s=document.all.item( this.m_flagId ).style + s.display="none" + if( fVal ) + s.display="" + else + s.display="none" +} + +var gHiliteClr="THREEDHIGHLIGHT",gShadowClr="THREEDSHADOW",gFaceClr="THREEDFACE" +var gBtnArr = new Array() +gBtnArr["nb_otl"] = new TxtBtn( "nb_otl","nb_otlElem",parent.ToggleOtlPane,GetOtlState ) +gBtnArr["nb_nts"] = new TxtBtn( "nb_nts","nb_ntsElem",parent.ToggleNtsPane,GetNtsState ) +gBtnArr["nb_prev"]= new ImgBtn( "nb_prev","nb_prevBorder",30,parent.GoToPrevSld ) +gBtnArr["nb_next"]= new ImgBtn( "nb_next","nb_nextBorder",30,parent.GoToNextSld ) +gBtnArr["nb_sldshw"]= new ImgBtn( "nb_sldshw","nb_sldshwBorder",18,parent.FullScreen ) +gBtnArr["nb_voice"] = new ImgBtn( "nb_voice","nb_voiceBorder",18,parent.ToggleVNarration ) +gBtnArr["nb_otlTxt"]= new ImgBtn( "nb_otlTxt","nb_otlTxtBorder",23,parent.ToggleOtlText ) +gBtnArr["nb_nts"].m_flagId= "notes_flag" +gBtnArr["nb_nts"].SetFlag = NtsBtnSetFlag +gBtnArr["nb_otlTxt"].ChangeIcon= GetOtlTxtState +var sNext="Next",sPrev="Previous",sEnd="End Show",sFont="Arial", alwaysOn = false +function ShowMenu() +{ + BuildMenu(); + var doc=PPTSld.document.body,x=PPTSld.event.clientX+doc.scrollLeft,y=PPTSld.event.clientY+doc.scrollTop + + m = PPTSld.document.all.item("ctxtmenu") + m.style.pixelLeft=x + if( (x+m.scrollWidth > doc.clientWidth)&&(x-m.scrollWidth > 0) ) + m.style.pixelLeft=x-m.scrollWidth + + m.style.pixelTop=y + if( (y+m.scrollHeight > doc.clientHeight)&&(y-m.scrollHeight > 0) ) + m.style.pixelTop=y-m.scrollHeight + + m.style.display="" +} +function _CM() +{ + if( !parent.IsFullScrMode() && !alwaysOn) return; + + if(!PPTSld.event.ctrlKey) { + ShowMenu() + return false + } else + HideMenu() +} + +function processNavKPH(event) { + if ( PPTSld && (event.keyCode != 13 || !event.srcElement.href || event.srcElement.href == "" ) ) + return PPTSld._KPH(event); +} +function processNavClick() { + HideMenu(); + return true; +} +function BuildMenu() +{ + if( PPTSld.document.all.item("ctxtmenu") ) return + + var mObj=CreateItem( PPTSld.document.body ) +mObj.id="ctxtmenu" + var s=mObj.style + s.position="absolute" + s.cursor="default" + s.width="100px" + SetCMBorder(mObj,"menu","black") + + var iObj=CreateItem( mObj ) + SetCMBorder( iObj, "threedhighlight","threedshadow" ) + iObj.style.padding=2 + if ( self.IsFullScrMode() ) { + CreateMenuItem( iObj,sNext,M_GoNextSld,M_True ) + CreateMenuItem( iObj,sPrev,M_GoPrevSld,M_HasPrevSld ) + } + else { + CreateMenuItem( iObj,sNext, base.TP_GoToNextSld, base.HasNextSld ) + CreateMenuItem( iObj,sPrev,base.GoToPrevSld, base.HasPrevSld ) + } + var sObj=CreateItem( iObj ) + SetCMBorder(sObj,"menu","menu") + var s=sObj.style + s.borderTopColor="threedshadow" + s.borderBottomColor="threedhighlight" + s.height=1 + s.fontSize="0px" + if ( self.IsFullScrMode() ) + CreateMenuItem( iObj,sEnd,M_End,M_True ) + else + CreateMenuItem( iObj,sEnd,M_End,M_False ) +} +function Highlight() { ChangeClr("activecaption","threedhighlight") } +function Deselect() { ChangeClr("threedface","menutext") } +function Perform() +{ + e=PPTSld.event.srcElement + if( e.type=="menuitem" && e.IsActive() ) + e.Action() + else + PPTSld.event.cancelBubble=true +} +function ChangeClr( bg,clr ) +{ + e=PPTSld.event.srcElement + if( e.type=="menuitem" && e.IsActive() ) { + e.style.backgroundColor=bg + e.style.color=clr + } +} + +function M_HasPrevSld() { return( base.HasPrevSld() ) } +function M_GoNextSld() { + base.SetFSMode(1); + if( gIsEndShow ) + M_End(); + else { + if ( base.HasNextSld() ) + base.GoToNextSld(); + else if ( base.EndSlideShow ) { + StartEndShow(); + gIsEndShow = 1; + + PPTNav.location.reload(); + } + else + base.CloseFullScreen(); + } +} +function M_GoPrevSld() { + base.SetFSMode(1); + g_hideNav = 0; + if( gIsEndShow ) { + gIsEndShow = 0; + if ( base.msie > 0 && IsMac() ) + ChangeFrame( SLIDE_FRAME, GetHrefObj( g_currentSlide ).m_slideHref ); + else + PPTSld.history.back(); + + PPTNav.location.reload(); + if( PPTSld.event ) + PPTSld.event.cancelBubble=true; + } + else + base.GoToPrevSld(); +} +function M_True() { return true } +function M_False() { return false } + +function M_End() { + base.CloseFullScreen(); + /*PPTSld.event.cancelBubble=true; + window.close( self )*/ +} + +function CreateMenuItem( node,text,action,eval ) +{ + var e=CreateItem( node ) + e.type="menuitem" + e.Action=action + e.IsActive=eval + e.innerHTML=text + + if( !e.IsActive() ) + e.style.color="threedshadow" + e.onclick=Perform + e.onmouseover=Highlight + e.onmouseout=Deselect + s=e.style; + s.fontFamily=sFont + s.fontSize="8pt" + s.paddingLeft=2 +} +function CreateItem( node ) +{ + var elem=PPTSld.document.createElement("DIV") + node.insertBefore( elem ) + return elem +} +function SetCMBorder( o,ltClr,rbClr ) +{ + var s=o.style + s.backgroundColor="menu" + s.borderStyle="solid" + s.borderWidth=1 + s.borderColor=ltClr+" "+rbClr+" "+rbClr+" "+ltClr +} + +/* netscape context menu */ +g_ctxmenu = 0; +function setRect( obj, X, Y, W, H ) { + obj.top = Y; + obj.left = X; + obj.clip.top = 0; + obj.clip.left = 0; + obj.clip.bottom = H; + obj.clip.right = W; +} + +function KPH(event) { + if ( ! base.IsFullScrMode() && !alwaysOn ) + return true; + + if ( (!IsMac() &&event.which == 3) || ( IsMac() && (event.modifiers & Event.CONTROL_MASK) && event.which == 1 ) ) { + PPTSld.g_ctxmenu = 1; + PPTSld.stripUobj.visibility = "show"; + PPTSld.stripDobj.visibility = "show"; + PPTSld.shadeUobj.visibility = "show"; + PPTSld.shadeDobj.visibility = "show"; + PPTSld.panelobj.visibility = "show"; + PPTSld.Fobj.visibility = "show"; + PPTSld.Bobj.visibility = "show"; + PPTSld.Eobj.visibility = "show"; + + setRect(PPTSld.shadeUobj, event.pageX-2, event.pageY-2, 82, 67 ); + setRect(PPTSld.shadeDobj, event.pageX, event.pageY, 82, 67 ); + setRect(PPTSld.panelobj, event.pageX, event.pageY, 80, 65 ); + setRect(PPTSld.Fobj, event.pageX, event.pageY, 80, 20 ); + setRect(PPTSld.Bobj, event.pageX, event.pageY+20, 80, 20 ); + setRect(PPTSld.stripUobj, event.pageX, event.pageY+41, 80, 1 ); + setRect(PPTSld.stripDobj, event.pageX, event.pageY+43, 80, 1 ); + setRect(PPTSld.Eobj, event.pageX, event.pageY+45, 80, 20 ); + return false; + } + if ( HitOK( event ) ) { + PPTSld.g_ctxmenu = 0; + PPTSld.stripUobj.visibility = "hide"; + PPTSld.stripDobj.visibility = "hide"; + PPTSld.shadeUobj.visibility = "hide"; + PPTSld.shadeDobj.visibility = "hide"; + PPTSld.panelobj.visibility = "hide"; + PPTSld.Fobj.visibility = "hide"; + PPTSld.Bobj.visibility = "hide"; + PPTSld.Eobj.visibility = "hide"; + } + return true; +} + +function overMe() { + this.bgColor = "blue"; +} + +function outMe() { + this.bgColor = "#AAAAAA"; +} + +function makeElement( whichEl, whichContainer ) { + if ( arguments.length == 1 ) { + whichContainer = PPTSld; + } + tmp = new Layer(100,whichContainer); + eval( whichEl + " = tmp" ); + return eval(whichEl); +} + +function initMe( obj, clr, text ) { + obj.bgColor = clr; +// obj.document.write("<a href='javascript:return false'>" + text + "</a>"); + obj.document.write( "<font size=2 face=Arial " ); + if ( !M_HasPrevSld() && (obj == PPTSld.Bobj ) ) { + obj.document.write( " color='#808080' " ); + } + else { + obj.onmouseover = overMe; + obj.onmouseout = outMe; + } + obj.document.write( " >   " + text +"</font> <layer top=0 left=0 width=100 height=40 ></layer>"); + obj.document.close(); + obj.captureEvents(Event.CLICK); + obj.color = "black"; +} + +function createCM() { + if ( base.IsFullScrMode() ) { + var clr = "#AAAAAA"; + PPTSld.shadeUobj = makeElement("SHADEU"); + PPTSld.shadeDobj = makeElement("SHADED"); + PPTSld.panelobj = makeElement("PANEL"); + PPTSld.stripUobj = makeElement("STRIPU"); + PPTSld.stripDobj = makeElement("STRIPD"); + PPTSld.shadeUobj.bgColor = "#BBBBBB"; + PPTSld.shadeDobj.bgColor = "#888888"; + PPTSld.stripUobj.bgColor = "#777777"; + PPTSld.stripDobj.bgColor = "#CCCCCC"; + PPTSld.panelobj.bgColor = clr; + PPTSld.Fobj = makeElement("Next"); + PPTSld.Bobj = makeElement("Previous"); + PPTSld.Eobj = makeElement("EndShow"); + initMe( PPTSld.Fobj, clr, "Next" ); + PPTSld.Fobj.onclick = M_GoNextSld; + + initMe( PPTSld.Bobj, clr, "Previous" ); + PPTSld.Bobj.onclick = M_GoPrevSld; + + initMe( PPTSld.Eobj, clr, "End Show"); + PPTSld.Eobj.onclick = base.CloseFullScreen; + } +} + +function IsContextMenu() { + return (g_ctxmenu == 1) +} +var g_notesTable = new Array() +var g_hiddenSlide = new Array() +makeSlide( 0,1,1); +makeSlide( 1,1,1); +makeSlide( 2,1,1); +makeSlide( 3,1,1); +makeSlide( 4,1,1); +makeSlide( 5,1,1); +makeSlide( 6,1,1); +makeSlide( 7,1,1); +makeSlide( 8,1,1); +makeSlide( 9,1,1); +makeSlide( 10,1,1); +makeSlide( 11,1,1); +makeSlide( 12,1,1); +makeSlide( 13,1,1); +makeSlide( 14,1,1); +makeSlide( 15,1,1); +makeSlide( 16,0,1); +makeSlide( 17,1,1); + +var END_SHOW_HREF = "endshow.htm", + OUTLINE_EXPAND_HREF = "outline_expanded.htm", + OUTLINE_COLLAPSE_HREF = "outline_collapsed.htm", + OUTLINE_NAVBAR_HREF = "outline_navigation_bar.htm", + NAVBAR_HREF = "navigation_bar.htm", + BLANK_NOTES_HREF = "blank_notes.htm", + NUM_VISIBLE_SLIDES = 18, + SIMPLE_FRAMESET = 0, + SLIDE_FRAME = "PPTSld", + NOTES_FRAME = "PPTNts", + OUTLINE_FRAME = "PPTOtl", + OUTLINE_NAVBAR_FRAME = "PPTOtlNav", + NAVBAR_FRAME = "PPTNav", + MAIN_FRAME = "MainFrame", + FS_NAVBAR_HREF = "fs_navigation_bar.htm", + isIEFiles = 2, + isNAVFiles = 8, + isFLATFiles = 16, + includeNotes = 1, + PPTPRESENTATION = 1; +var INITSLIDENUM = 1; + +var EndSlideShow = 0; +var g_outline_href = OUTLINE_COLLAPSE_HREF; +var g_fullscrMode = 0; +var FSWin = null; +var gtmpstr = document.location.href; +var g_baseURL = gtmpstr.substr(0, gtmpstr.lastIndexOf("/") ) + "/" + "webqtl_demo2_part1.ppt_files"; +var g_showoutline = 1; +var g_shownotes = includeNotes; +var g_currentSlide = INITSLIDENUM, g_prevSlide = INITSLIDENUM; +var saveFSSlideNum = saveTPSlideNum = g_currentSlide; +var saveFSprevSlide = saveTPprevSlide = g_prevSlide; +var g_slideType="ie"; +var appVer = navigator.appVersion; +var msie = appVer.indexOf( "MSIE " ) + appVer.indexOf( "Internet Explorer " ); +var isnav = ( navigator.appName.indexOf( "Netscape" ) >= 0 ); +var msieWin31 = (appVer.indexOf( "Windows 3.1" ) > 0); +var ver = 0; +var g_done = 0; +var g_prevotlobjidx = 0; +var g_ShowFSDefault = 0; +var g_lastVisibleSld = 1; +var g_allHidden = false; +function IsIE() { + return (msie >= 0 ); +} + +function IsNav() { + return (isnav); +} +var msiePos = appVer.indexOf( "MSIE " ); +var inexPos = appVer.indexOf( "Internet Explorer " ); +if ( msiePos >= 0 ) + ver = parseFloat( appVer.substring( msiePos+5, appVer.indexOf ( ";", msiePos ) ) ); +else if( inexPos >= 0 ) + ver=parseFloat( appVer.substring( inexPos+18, appVer.indexOf(";",inexPos) ) ) +else + ver = parseInt( appVer ); + +//var g_supportsPPTHTML = 0; //!msieWin31 && ( ( msie >= 0 && ver >= 3.02 ) || ( msie < 0 && ver >= 3 ) ); + +function GetCurrentSlideNum() +{ + obj = GetHrefObj( g_currentSlide ); + if ( GetHrefObj( g_currentSlide ).m_origVisibility == 1 ) + return obj.m_slideIdx; + else + return g_currentSlide; +} + +function GetNumSlides() +{ + if ( GetHrefObj( g_currentSlide ).m_origVisibility == 1 ) + return NUM_VISIBLE_SLIDES; + else + return g_docTable.length; +} + +function GetHrefObj( slideIdx ) +{ return g_docTable[slideIdx - 1]; +} + +function GetSlideNum( slideHref ) +{ + for (ii=0; ii<g_docTable.length; ii++) { + if ( g_docTable[ii].m_slideHref == slideHref ) + return ii+1; + } + return 1; +} + +function GoToNextSld() +{ + targetIdx = g_currentSlide + 1; + if ( GetHrefObj( targetIdx-1 ).m_origVisibility == 0 ) { + if ( targetIdx<=g_docTable.length ) { + obj = GetHrefObj( targetIdx ); + obj.m_visibility = 1; + GoToSld( obj.m_slideHref ); + } + } + else { + obj = GetHrefObj( targetIdx ); + while ( obj && ( obj.m_origVisibility == 0 ) && ( targetIdx<=g_docTable.length ) ) + obj = GetHrefObj( targetIdx++ ); + if( obj && obj.m_origVisibility ) + GoToSld( obj.m_slideHref ); + } +} + +function GoToPrevSld() +{ + targetIdx = g_currentSlide - 1; + if ( targetIdx > 0 ) { + obj = GetHrefObj( targetIdx ); + while ( ( obj.m_visibility == 0 ) && ( targetIdx>0 ) ) + obj = GetHrefObj( targetIdx-- ); + GoToSld( obj.m_slideHref ); + } +} + +function GoToLast() +{ + targetIdx = g_docTable.length; + if ( targetIdx != g_currentSlide ) + GoToSld( GetHrefObj( targetIdx ).m_slideHref ); +} + +function GoToFirst() +{ GoToSld( GetHrefObj(1).m_slideHref ); +} + +function highlite() { + if ( IsFullScrMode() ) + return; + index = GetCurrentSlideNum(); + if ( !frames[MAIN_FRAME].frames[OUTLINE_FRAME] ) + return; + if ( msie < 0 ) { + if ( g_prevotlobjidx != 0 ) { + eval( "otlobj = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.LAYERID" + g_prevotlobjidx ); + otlobj.hidden = true; + } + else + index = GetCurrentSlideNum(); + eval( "otlobj = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.LAYERID" + index ); + otlobj.hidden = false; + + g_prevotlobjidx = index; + + return; + } + if ( !g_showoutline ) + return; + + backclr = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.body.bgColor; + textclr = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.body.text; + if ( g_prevotlobjidx != 0 ) { + eval( "otlobj = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.all.p" + g_prevotlobjidx ); + otlobj.style.backgroundColor = backclr; + otlobj.style.color = textclr; + otlobj.all.AREF.style.color = textclr; + } + else + index = GetCurrentSlideNum(); + eval( "otlobj = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.all.p" + index ); + otlobj.style.backgroundColor = textclr; + otlobj.style.color = backclr; + otlobj.all.AREF.style.color = backclr; + g_prevotlobjidx = index; +} + +function ChangeFrame( frame, href ) +{ +if ( IsFramesMode() ) { + if ( NAVBAR_FRAME == frame || OUTLINE_NAVBAR_FRAME == frame ) { + frames[frame].location.replace(href); + } + else if( ! ( ( OUTLINE_FRAME == frame && !g_showoutline) || (NOTES_FRAME == frame && !g_shownotes ) ) ){ + frames[MAIN_FRAME].frames[frame].location.href = href; + } + } + else { + if ( frame == NAVBAR_FRAME || frame == SLIDE_FRAME ) { + if( frame == NAVBAR_FRAME ) { + href = FS_NAVBAR_HREF; + + } + if( frame == NAVBAR_FRAME ) + window.frames[frame].location.replace(href); + else + window.frames[frame].location.href = href; + } + } + +} + +function shutEventPropagation() { + if ( IsNav() ) + return; + + var slideFrame; + if ( IsFramesMode() ) + slideFrame = frames[MAIN_FRAME].frames[SLIDE_FRAME]; + else + slideFrame = window.frames[SLIDE_FRAME]; + if ( slideFrame.event ) + slideFrame.event.cancelBubble=true; +} + +function GoToSld( slideHref ) +{ + shutEventPropagation(); + if ( slideHref != GetHrefObj( g_currentSlide ).m_slideHref || g_slideType != GetHrefObj( g_currentSlide ).type) { + g_prevSlide = g_currentSlide; + g_currentSlide = GetSlideNum( slideHref ); + g_slideType = GetHrefObj( g_currentSlide ).type; + obj = GetHrefObj( g_currentSlide ); + obj.m_visibility = 1; + ChangeFrame( SLIDE_FRAME, slideHref ); + if( !SIMPLE_FRAMESET ) + ChangeFrame( NOTES_FRAME, obj.m_notesHref ); + ChangeFrame( NAVBAR_FRAME, NAVBAR_HREF ); + + } +} + +function PrevSldViewed() +{ GoToSld( GetHrefObj( g_prevSlide ).m_slideHref ); +} + +function NoHref() {} + +function ExpandOutline( ) +{ + g_outline_href = OUTLINE_EXPAND_HREF; + ChangeFrame( OUTLINE_FRAME, OUTLINE_EXPAND_HREF ); + frames[OUTLINE_NAVBAR_FRAME].location.replace( OUTLINE_NAVBAR_HREF); +} + +function CollapseOutline() +{ + g_outline_href = OUTLINE_COLLAPSE_HREF; + ChangeFrame( OUTLINE_FRAME, OUTLINE_COLLAPSE_HREF ); + frames[OUTLINE_NAVBAR_FRAME].location.replace( OUTLINE_NAVBAR_HREF); + } + +function SlideUpdated( id ) +{ + if ( id != GetHrefObj( g_currentSlide ).m_slideHref ) { + g_prevSlide = g_currentSlide; + g_currentSlide = GetSlideNum( id ); + obj = GetHrefObj( g_currentSlide ); + if( !SIMPLE_FRAMESET ) + ChangeFrame( NOTES_FRAME, obj.m_notesHref ); + ChangeFrame( NAVBAR_FRAME, NAVBAR_HREF ); + } +} + +function hrefList( slideHref, notesHref, visible, slideIdx, type ) +{ + this.m_slideHref = slideHref; + this.m_notesHref = notesHref; + this.m_navbarHref = NAVBAR_HREF; + this.m_origVisibility = visible; + this.m_visibility = visible; + this.m_slideIdx = slideIdx; + this.type = type; +} + +function IsFullScrMode() { + return g_fullscrMode; +} + + +function IsFramesMode() { + return (1 - g_fullscrMode); +} + +function SldUpdated( id ) +{ + if ( ( id != GetHrefObj( g_currentSlide ).m_slideHref ) || ( g_currentSlide == g_lastVisibleSld ) ){ + g_prevSlide = g_currentSlide; + g_currentSlide = GetSlideNum( id ); + obj = GetHrefObj( g_currentSlide ); + if( !SIMPLE_FRAMESET ) + ChangeFrame( NOTES_FRAME, obj.m_notesHref ); + ChangeFrame( NAVBAR_FRAME, NAVBAR_HREF ); + } +} + +function ToggleOutline() { + g_showoutline = 1 - g_showoutline; + writeMyFrame(); +} + +function ShowHideNotes() { + g_shownotes = 1 - g_shownotes; + writeMyFrame(); +} + +function writeMyFrame() { + SetFSMode(0); + obj = frames[MAIN_FRAME]; + + var curslide = g_baseURL + "/" + GetHrefObj( g_currentSlide ).m_slideHref; + var curnotes = g_baseURL + "/" + GetHrefObj( g_currentSlide ).m_notesHref; + var otlhref = g_baseURL + "/" + g_outline_href; + if ( msie < 0 ) { + if ( ! g_showoutline && g_shownotes ) { + obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \ + <frameset rows=\"*,20%\" id=\"frameset2\" > \ + <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \ + <frame src=\"' + curnotes + '\" name=PPTNts marginheight=0 marginwidth=0> \ + </frameset> </html>' ); + } + else if( g_showoutline && g_shownotes ){ + obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \ + <frameset cols=\"20%,*\" id=\"frameset1\"> \ + <frame src=\"' + otlhref + '\" name=PPTOtl> \ + <frameset rows=\"*,20%\" id=\"frameset2\" > \ + <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \ + <frame src=\"' + curnotes + '\" name=PPTNts marginheight=0 marginwidth=0> \ + </frameset> </frameset></html>' ); + } + else if ( !g_shownotes && !g_showoutline ) { + obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \ + <frameset rows="*,0" frameborder=0 > \ + <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \ + </frameset> </html>' ); + } + else if( !g_shownotes && g_showoutline ) { + obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \ + <frameset cols=\"20%,*\" id=\"frameset1\"> \ + <frame src=\"' + otlhref + '\" name=PPTOtl> \ + <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \ + </frameset></html>' ); + } + obj.document.close(); + } + else { + if ( g_showoutline ) { + obj.PPTHorizAdjust.cols = "20%,*"; + obj.PPTOtl.location.reload(); + } + else { + obj.PPTHorizAdjust.cols = "0,*"; + } + if ( g_shownotes ) { + obj.PPTVertAdjust.rows = "*,20%"; + obj.PPTNts.location.href = curnotes; + } + else { + obj.PPTVertAdjust.rows = "*,0"; + } + } + ChangeFrame( OUTLINE_NAVBAR_FRAME, OUTLINE_NAVBAR_HREF ); +} + +function FullScreen() { + g_done = 0; + + + SetFSMode(1); + if ( msie >= 0 ) + FSWin = window.open( g_baseURL + "/" + "fullscreen.htm", null, "fullscreen=yes"); + else { + var height = screen.availHeight; + if ( window.navigator.platform.indexOf( "Mac" ) >= 0 ) { + height -= 30; + } + FSWin = window.open( g_baseURL + "/" + "fullscreen.htm", "null", "height="+ height + ",width=" + screen.availWidth + ",screenX=0,screenY=0"); + } +} + +function SetFSMode( i ) { + +} + +function Slide( i ) { + SetFSMode(0); + GoToSld(GetHrefObj(i).m_slideHref); +} + +function TP_GoToNextSld() { + SetFSMode(0); + GoToNextSld(); +} + +function TP_GoToPrevSld() { + SetFSMode(0); + GoToPrevSld(); +} + +function CloseFullScreen() { + g_done = 0; + + if ( IsNav() ){ + if ( self.opener ) + opener.FSWin = null; + } + window.close(); +} + +function slidenum(i) { + var slidename = "slide"; + if ( i < 10 ) + return ( slidename + "000" + i); + else if ( i < 100 ) + return ( slidename + "00" + i ); + else if ( i < 1000 ) + return (slidename + "0" + i ); + else + return (slidename + i ); +} +function UpdateLastVisibleSlide( index ) { + if ( g_lastVisibleSld < index ) + g_lastVisibleSld = index; +} + +function jpegArray( numSlides ) { +count_hidden = 0; + g_docTable = new Array(); + for( i=0; i<numSlides; i++ ) { + j = 2 * numSlides + i + 1; + var str = slidenum( j ) +".htm"; + if( g_notesTable[i] == 1 ) + g_docTable[i] = new hrefList( str, slidenum(i+1 ) + "_notes_pane.htm", g_hiddenSlide[i], i+1-count_hidden, "jpeg" ); + else + g_docTable[i] = new hrefList( str, BLANK_NOTES_HREF, g_hiddenSlide[i], i+1-count_hidden, "jpeg" ); + if ( !g_hiddenSlide[i] ) count_hidden++; + else UpdateLastVisibleSlide( i+1 ); + } +} + +function ieArray( numSlides ) { +count_hidden = 0; + g_docTable = new Array(); + for( i=0; i<numSlides; i++ ) { + var str = slidenum(i+1) +".htm"; + if( g_notesTable[i] == 1 ) + g_docTable[i] = new hrefList( str, slidenum( i+1 ) + "_notes_pane.htm", g_hiddenSlide[i], i+1-count_hidden, "ie" ); + else + g_docTable[i] = new hrefList( str, BLANK_NOTES_HREF, g_hiddenSlide[i], i+1-count_hidden, "ie" ); + if ( !g_hiddenSlide[i] ) count_hidden++; + else UpdateLastVisibleSlide( i+1 ); + } +} + +function navArray( numSlides ) { +count_hidden = 0; + g_docTable = new Array(); + for( i=0; i<numSlides; i++ ) { + j = numSlides + i + 1; + var str = slidenum( j ) +".htm"; + if( g_notesTable[i] == 1 ) + g_docTable[i] = new hrefList( str, slidenum(i+1 ) + "_notes_pane.htm", g_hiddenSlide[i], i+1-count_hidden, "nav" ); + else + g_docTable[i] = new hrefList( str, BLANK_NOTES_HREF, g_hiddenSlide[i], i+1-count_hidden, "nav" ); + if ( !g_hiddenSlide[i] ) count_hidden++; + else UpdateLastVisibleSlide( i+1 ); + } +} + +function LoadHTMLVersion() { + var os = window.navigator.platform.indexOf("Mac"); + if ( (msie || isnav ) && ( (os < 0 && ver >= 4 ) || ( os >= 0 && ver >= 5 ) || (os >=0 && msie < 0 && ver >= 4 ) ) ){ + if ( msie >= 0 ) { + if ( isIEFiles > 0 ) + ieArray( 18 ); + else if ( isFLATFiles > 0 ){ + /*if ( IsFramesMode() ) + StatusPlay("This presentation is optimized for use with older versions of your browser. Since you are using a more recent version of Microsoft Internet Explorer or Netscape Navigator, consider optimizing this presentation to take advantage of your current version's advanced capabilities."); */ + jpegArray( 18 ); + } + else + window.location.replace( "webqtl_demo2_part1.ppt_files/error.htm" ); + } + else { + if ( isNAVFiles > 0 && ver < 5) + navArray( 18 ); + else if ( isFLATFiles > 0 ) { + /* if ( IsFramesMode() ) + StatusPlay("This presentation is optimized for use with older versions of your browser. Since you are using a more recent version of Microsoft Internet Explorer or Netscape Navigator, consider optimizing this presentation to take advantage of your current version's advanced capabilities."); */ + jpegArray( 18 ); + } + else + window.location.replace( "webqtl_demo2_part1.ppt_files/error.htm" ); + } +} +else { + /* + if ( IsFramesMode() && !isWebTV() ) + StatusPlay("This presentation contains content that your browser may not be able to show properly. This presentation was optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator."); + */ + if ( isFLATFiles <= 0 ) { + /* if ( IsFramesMode() ) + window.alert("This presentation contains content that your browser may not be able to display properly. This presentation is optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator." ); + */ + window.location.replace( "webqtl_demo2_part1.ppt_files/error.htm" ); + } + /* + else if ( IsFramesMode() && !isWebTV() ) + StatusPlay( "This presentation contains content that your browser may not be able to show properly. This presentation was optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator." ); + */ + jpegArray ( 18 ); + } + +} + +function isWebTV() { + if ( window.navigator.appName.indexOf( 'WebTV' ) >= 0 ) + return true; + return false; +} + +var count; +var statusText; +var statusfirst = 0; + function display50( text ) +{ + len = text.length; + if ( len < 50 && count < 2) { + window.status = text; + window.setTimeout( "repeat()", 300 ); + } + else { + var period = 200; + window.status = text; + newtext = text.substring( 1, len ); + if ( statusfirst ) { + statusfirst = 0; + period = 2000; + } + window.setTimeout( "display50( newtext )", period ); + } +} +function repeat( ) { + count++; + statusfirst = 1; + display50( statusText ); +} + +function StatusPlay( text ) { + count = 0; + statusText = text; + repeat( ); + } +function makeSlide( i, notes, visible ) { + g_notesTable[i] = notes; + g_hiddenSlide[i] = visible; +} + diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001.htm new file mode 100755 index 00000000..d17c2490 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: GeneNetwork and WebQTL:"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0001.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:.88%;left:3.31%;width:84.37%;height:9.89%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-277 0 -1";mso-margin-left-alt:232; mso-text-indent-alt:0;position:absolute;top:0%;left:1.25%;width:97.95%; height:100.0%'><span style='font-size:105%'><i>GeneNetwork and WebQTL:</i></span><span style='font-size:68%;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </div> <div style='position:absolute;top:24.02%;left:5.82%;width:69.0%;height:50.7%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='position:absolute;top:0%;left:2.87%;width:97.12%; height:71.08%'> <div style='mso-line-spacing:"-256 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:0%;left:0%;width:92.68%;height:53.43%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='mso-special-format: nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size: 99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Part 1: How to study </span></span><span style='position:absolute;top:31.19%; left:8.1%;width:91.89%'><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>expression variation and </span></span><span style='position:absolute; top:61.46%;left:8.1%;width:91.89%'><span style='font-size:106%;color:#E9EB5D; mso-color-index:3'>covariation (slides 2–16)<br> </span></span></div> <div style='mso-line-spacing:"-256 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:63.23%;left:0%;width:100.0%;height:36.76%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='mso-special-format: nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size: 99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Part 2. Discovering upstream </span></span><span style='position:absolute; top:45.33%;left:7.5%;width:89.32%'><span style='font-size:106%;color:#E9EB5D; mso-color-index:3'>modulators (slides 17–30)</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></span></div> </div> </div> <img border=0 src="slide0001_image001.png" style='position:absolute;top:21.9%; left:74.56%;width:23.57%;height:64.31%'> <div class=O style='position:absolute;top:79.32%;left:75.89%;width:10.46%; height:14.48%'> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:42.68%'><span style='font-family:"Arial Rounded MT Bold";font-size:233%;color:#6E6E6E'>RNA</span><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; display:none'><br> </span></div> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:46.34%;left:0%;width:82.27%;height:54.87%'><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; mso-special-format:lastCR;display:none'><br> </span></div> </div> <div class=O style='position:absolute;top:66.43%;left:3.44%;width:80.66%; height:11.48%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'><i>PowerPoint ÒNormal viewÓ has notes that may be </i></span></span><span style='position:absolute;top:50.76%;left:0%;width:86.53%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'><i>useful companions to these slides.</i></span><span style='font-family: "Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:3;mso-special-format: lastCR;display:none'><br> </span></span></div> <div class=O style='position:absolute;top:10.95%;left:6.35%;width:55.23%; height:7.42%'><span style='font-family:"Gill Sans";font-size:283%;color:#E9EB5D'><i>a PowerPoint Presentation</i></span><span style='font-family:"Gill Sans"; font-size:317%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></div> <div class=O style='position:absolute;top:92.4%;left:75.23%;width:26.49%; height:3.88%'><span style='font-family:Helvetica;font-size:167%;color:#E9EB5D'><i>RWW 07.23.2005</i></span></div> <div class=O style='position:absolute;top:81.97%;left:3.44%;width:77.21%; height:11.48%'> <div style='position:absolute;top:0%;left:0%;width:88.16%;height:49.23%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'><i>You can also download this PowerPoint at<br> </i></span></div> <div style='position:absolute;top:50.76%;left:0%;width:100.0%;height:49.23%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'><i>ftp://atlas.utmem.edu/public/webqtl_demo2.ppt </i></span><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Welcome to a short demonstration of the GeneNetwork and its WebQTL module. Please adjust the size of the windows on your monitor so that you can see part of this page, as well as GeneNetwork windows. WebQTL produces a large number of new windows, so you may need to modify your browser preferences to permit pop-ups. In this demonstration, we explore one important transcript expressed in the brain: the amyloid beta precursor protein messenger RNA. A protein product of this mRNA, the APP protein, is associated with AlzheimerÕs disease.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>My thanks to Dr. Robert F. Clark and Wenli Cai for testing this PowerPoint demonstration and making many improvements.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>(Initial version of June 2003 by Rob Williams. Edits July 13, 2005 by RW and RFC. Edit July 14, 2005 by WC. Final edits by RF Clark, July 22, 2005.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001_image001.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001_image001.png new file mode 100755 index 00000000..a1cb20e4 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001_image001.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001_notes_pane.htm new file mode 100755 index 00000000..7c670210 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Welcome to a short demonstration of the GeneNetwork and its WebQTL module. Please adjust the size of the windows on your monitor so that you can see part of this page, as well as GeneNetwork windows. WebQTL produces a large number of new windows, so you may need to modify your browser preferences to permit pop-ups. In this demonstration, we explore one important transcript expressed in the brain: the amyloid beta precursor protein messenger RNA. A protein product of this mRNA, the APP protein, is associated with AlzheimerÕs disease.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>My thanks to Dr. Robert F. Clark and Wenli Cai for testing this PowerPoint demonstration and making many improvements.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>(Initial version of June 2003 by Rob Williams. Edits July 13, 2005 by RW and RFC. Edit July 14, 2005 by WC. Final edits by RF Clark, July 22, 2005.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002.htm new file mode 100755 index 00000000..8627e129 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0002.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img border=0 src="slide0002_image002.png" style='position:absolute;top:8.3%; left:.39%;width:86.35%;height:86.21%'><img border=0 src="slide0002_image003.png" style='position:absolute;top:34.27%;left:59.07%;width:12.18%;height:14.48%'> <div style='position:absolute;top:46.64%;left:85.43%;width:16.29%;height:12.01%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:2.94%;left:5.69%;width:93.49%; height:91.17%'> <div style='mso-line-spacing:"-224 0 0";position:absolute;top:0%;left:0%; width:91.3%;height:51.61%'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>Choose<br> </span></div> <div style='mso-line-spacing:"-224 0 0";position:absolute;top:48.38%; left:0%;width:100.0%;height:51.61%'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'>database</span></div> </div> </div> <div style='position:absolute;top:62.19%;left:86.62%;width:21.05%;height:12.72%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:6.94%;left:5.03%;width:89.93%; height:86.11%'> <div style='position:absolute;top:0%;left:0%;width:100.0%;height:51.61%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>Enter<br> </span></div> <div style='mso-line-spacing:"-224 0 0";position:absolute;top:48.38%; left:0%;width:100.0%;height:51.61%'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'><i>APP</i></span><span style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D;mso-color-index: 3;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </div> </div> <div style='position:absolute;top:77.73%;left:85.96%;width:12.58%;height:12.72%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:6.94%;left:8.42%;width:91.57%; height:86.11%'> <div style='position:absolute;top:0%;left:0%;width:91.95%;height:51.61%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>Select<br> </span></div> <div style='mso-line-spacing:"-224 0 0";position:absolute;top:48.38%; left:0%;width:100.0%;height:51.61%'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'>search</span></div> </div> </div> <div style='position:absolute;top:.88%;left:0%;width:111.92%;height:9.18%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div style='position:absolute;top:0%;left:.94%;width:99.05%;height:80.76%'> <div class=B1 style='mso-margin-left-alt:644;mso-text-indent-alt:420'></div> <div class=B2 style='mso-margin-left-alt:937;mso-text-indent-alt:716'></div> <div class=B3 style='mso-margin-left-alt:1232;mso-text-indent-alt:1009'></div> <div class=B4 style='mso-margin-left-alt:1544;mso-text-indent-alt:1304'></div> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:0;position:absolute;top:0%;left:0%;width:100.0%;height: 100.0%'><span style='mso-special-format:nobullet;display:none;color:#FBFDB8; font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size: 106%;color:#E9EB5D;mso-color-index:3'>PART 1: How to study variation and covariation</span></div> </div> </div> <div style='position:absolute;top:15.54%;left:85.82%;width:16.15%;height:22.43%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='mso-line-spacing:"-224 0 0";position:absolute;top:1.57%; left:6.55%;width:94.26%;height:94.48%'><span style='position:absolute; top:0%;left:0%;width:91.3%'><span style='font-family:"Gill Sans";font-size: 217%;color:#E9EB5D;mso-color-index:3'>Choose<span style="mso-spacerun: yes"> </span></span></span><span style='position:absolute;top:25.0%; left:0%;width:91.3%'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>species, </span></span><span style='position: absolute;top:49.16%;left:0%;width:91.3%'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'>group, </span></span><span style='position:absolute;top:73.33%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>and type</span></span></div> </div> <img border=0 src="slide0002_image004.png" style='position:absolute;top:71.37%; left:48.87%;width:12.58%;height:13.78%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Please link to the web site:<span style="mso-spacerun: yes"> </span>http://www.genenetwork.org</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>To begin a search you make choices about what species, group, and database to explore.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>For this demonstration enter APP as above and click on the SEARCH button. Make sure that the DEFAULT SETTINGS are species = Mouse, Group = BXD, Type = Whole Brain, and Database = INIA BRAIN mRNA M430 (Apr05) PDNN.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. The GeneNetwork and WebQTL are often used to work with public data sets. However, it is possible to enter and analyze your own data for specific genetic reference populations such as the BXD genetic reference population of mice or the HXB strains of rat. Entering your own data is a more advanced topic, but if you click on the HOME pop-down menu (upper left), you will see ÒEnter Trait DataÓ that will explain the process.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>2.</font><font face=Helvetica size=3> For help on advanced searching methods read the left side of the page (INTRODUCTION).<span style="mso-spacerun: yes"> </span>If you make a search term too complex, you may get no hits (try entering Òamyloid betaÓ for example). If you make it too simple, you may also get too many.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>3.</font><font face=Helvetica size=3> Use the asterisk * as a wildcard. For example, to find all <i>Hoxb</i> transcripts, search for Hoxb*.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>4.</font><font face=Helvetica size=3> In some cases you can also research for transcripts and genes using special search strings such as Ò</font><font face=Geneva size=3>Mb = (Chr1, 100 102)Ó to find all genes on Chromosome 1 between 98 and 104 megabases (donÕt actually use the quotes). Details are described at </font><font face=Verdana size=3>http://www.genenetwork.org/searchHelp.html</font><font face=Geneva size=3>.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>5.<span style="mso-spacerun: yes"> </span>These INFO buttons provide links to data about the different data types. Try them.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>6.<span style="mso-spacerun: yes"> </span>The SET TO DEFAULT button is used to change the database default setting to match your typical search categories.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image002.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image002.png new file mode 100755 index 00000000..2eb797be --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image002.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image003.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image003.png new file mode 100755 index 00000000..d1370484 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image003.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image004.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image004.png new file mode 100755 index 00000000..a4f088b8 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image004.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_notes_pane.htm new file mode 100755 index 00000000..5f7740c5 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Please link to the web site:<span style="mso-spacerun: yes"> </span>http://www.genenetwork.org</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>To begin a search you make choices about what species, group, and database to explore.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>For this demonstration enter APP as above and click on the SEARCH button. Make sure that the DEFAULT SETTINGS are species = Mouse, Group = BXD, Type = Whole Brain, and Database = INIA BRAIN mRNA M430 (Apr05) PDNN.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>1. The GeneNetwork and WebQTL are often used to work with public data sets. However, it is possible to enter and analyze your own data for specific genetic reference populations such as the BXD genetic reference population of mice or the HXB strains of rat. Entering your own data is a more advanced topic, but if you click on the HOME pop-down menu (upper left), you will see ÒEnter Trait DataÓ that will explain the process.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>2.</font><font face=Helvetica size=2> For help on advanced searching methods read the left side of the page (INTRODUCTION).<span style="mso-spacerun: yes"> </span>If you make a search term too complex, you may get no hits (try entering Òamyloid betaÓ for example). If you make it too simple, you may also get too many.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>3.</font><font face=Helvetica size=2> Use the asterisk * as a wildcard. For example, to find all <i>Hoxb</i> transcripts, search for Hoxb*.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>4.</font><font face=Helvetica size=2> In some cases you can also research for transcripts and genes using special search strings such as Ò</font><font face=Geneva color="#222222" size=2>Mb = (Chr1, 100 102)Ó to find all genes on Chromosome 1 between 98 and 104 megabases (donÕt actually use the quotes). Details are described at </font><font face=Verdana color=black size=2>http://www.genenetwork.org/searchHelp.html</font><font face=Geneva color="#222222" size=2>.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>5.<span style="mso-spacerun: yes"> </span>These INFO buttons provide links to data about the different data types. Try them.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>6.<span style="mso-spacerun: yes"> </span>The SET TO DEFAULT button is used to change the database default setting to match your typical search categories.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003.htm new file mode 100755 index 00000000..5507bd68 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0003.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img border=0 src="slide0003_image005.png" style='position:absolute;top:34.27%; left:59.07%;width:12.18%;height:14.48%'> <div style='position:absolute;top:.88%;left:.79%;width:105.69%;height:9.18%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div style='position:absolute;top:0%;left:1.0%;width:98.99%;height:80.76%'> <div class=B1 style='mso-margin-left-alt:644;mso-text-indent-alt:420'></div> <div class=B2 style='mso-margin-left-alt:937;mso-text-indent-alt:716'></div> <div class=B3 style='mso-margin-left-alt:1232;mso-text-indent-alt:1009'></div> <div class=B4 style='mso-margin-left-alt:1544;mso-text-indent-alt:1304'></div> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:0;position:absolute;top:0%;left:0%;width:100.0%;height: 100.0%'><span style='mso-special-format:nobullet;display:none;color:#FBFDB8; font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size: 106%;color:#E9EB5D;mso-color-index:3'>Please also use the Glossary, FAQ, and News</span></div> </div> </div> <img border=0 src="slide0003_image006.png" style='position:absolute;top:10.07%; left:1.72%;width:69.66%;height:60.95%'><img border=0 src="slide0003_image008.png" style='position:absolute;top:9.18%;left:18.8%; width:12.58%;height:13.78%'><img border=0 src="slide0003_image009.png" style='position:absolute;top:49.11%;left:38.27%;width:60.0%;height:48.58%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>SHORT DETOUR to the HELP menu. If you are new to the GeneNetwork, you may find it helpful to review the The Glossary and FAQ pages shown above. We are in the process of making ÒliveÓ demos for some of the key modules in the GeneNetwork. Check the NEWS every month or two to find out about new features.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image005.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image005.png new file mode 100755 index 00000000..d1370484 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image005.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image006.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image006.png new file mode 100755 index 00000000..c9843a48 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image006.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image008.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image008.png new file mode 100755 index 00000000..504177df --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image008.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image009.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image009.png new file mode 100755 index 00000000..901c77a0 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image009.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_notes_pane.htm new file mode 100755 index 00000000..b8742fdc --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>SHORT DETOUR to the HELP menu. If you are new to the GeneNetwork, you may find it helpful to review the The Glossary and FAQ pages shown above. We are in the process of making ÒliveÓ demos for some of the key modules in the GeneNetwork. Check the NEWS every month or two to find out about new features.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004.htm new file mode 100755 index 00000000..ab2d96f6 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Search results"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0004.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img border=0 src="slide0004_image010.png" style='position:absolute;top:9.18%; left:3.31%;width:68.74%;height:90.81%'><img border=0 src="slide0004_image012.png" style='position:absolute;top:63.78%;left:63.57%; width:14.7%;height:6.53%'> <div class=O style='position:absolute;top:45.93%;left:80.13%;width:18.94%; height:47.17%'> <div style='mso-line-spacing:"-224 0 0";position:absolute;top:0%;left:0%; width:100.0%;height:44.94%'><span style='position:absolute;top:0%;left:0%; width:100.0%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'>Highlight </span></span><span style='position:absolute; top:24.16%;left:0%;width:100.0%'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'>this probe </span></span><span style='position:absolute;top:49.16%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>set in red </span></span><span style='position:absolute;top:73.33%; left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>and</span><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3;display:none'><i><br> </i></span></span></div> <div style='mso-line-spacing:"-224 0 0";position:absolute;top:43.82%; left:0%;width:100.0%;height:56.17%'><span style='position:absolute;top:0%; left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>click. You </span></span><span style='position:absolute;top:20.0%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>do NOT </span></span><span style='position:absolute;top:39.33%;left:0%; width:100.0%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'>have to </span></span><span style='position:absolute; top:59.33%;left:0%;width:100.0%'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'>select the </span></span><span style='position:absolute;top:78.66%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>checkbox</span><span style='font-family:"Gill Sans";font-size:250%; color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;display:none'><br> </span></span></div> </div> <div style='position:absolute;top:-4.41%;left:1.72%;width:84.63%;height:18.19%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='position:absolute;top:29.12%;left:1.4%;width:97.18%; height:42.71%'><span style='font-size:82%'>Search results</span><span style='mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>RESULTS OF THE APP SEARCH.<span style="mso-spacerun: yes"> </span>A search of the INIA Brain database generates 18 matches, 10 of which are shown above. The GeneNetwork will display several hundred matches in pages of 40 each. If a search generates a larger numbers of hits, then you will need to refine search terms.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. APP is a great transcript to introduce you to the complexity and power of new array platforms that often provide ÒalternativeÓ expression estimates for single genes. There are seven probe sets that target different parts of the APP transcript. Which of the alternative measurements is most appropriate and informative? Have a look at the FAQ page for more on this topic, but general advice: 1. be skeptical and try to validate that the correct transcript and gene is being measured; 2. check what part of the transcript is complementary to the probes; 3. evaluate the performance of individual probes based on expression level, signal-to-noise and other error terms such as the standard deviation and error.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. In this particular case we have highlighted and selected # 5 on this SEARCH RESULTS page. The annotation for this probe set mentions that it targets the last three exons and the 3Õ untranslated region (UTR) of the amyloid precursor protein (APP).<span style="mso-spacerun: yes"> </span>That is just what we want.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. Most probe sets have not been annotated in as much detail as App. Refer tot the FAQ to learn how to annotate probe sets yourself.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image010.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image010.png new file mode 100755 index 00000000..08c136e3 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image010.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image012.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image012.png new file mode 100755 index 00000000..b8e67f4d --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image012.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_notes_pane.htm new file mode 100755 index 00000000..f7336dcc --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>RESULTS OF THE APP SEARCH.<span style="mso-spacerun: yes"> </span>A search of the INIA Brain database generates 18 matches, 10 of which are shown above. The GeneNetwork will display several hundred matches in pages of 40 each. If a search generates a larger numbers of hits, then you will need to refine search terms.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>1. APP is a great transcript to introduce you to the complexity and power of new array platforms that often provide ÒalternativeÓ expression estimates for single genes. There are seven probe sets that target different parts of the APP transcript. Which of the alternative measurements is most appropriate and informative? Have a look at the FAQ page for more on this topic, but general advice: 1. be skeptical and try to validate that the correct transcript and gene is being measured; 2. check what part of the transcript is complementary to the probes; 3. evaluate the performance of individual probes based on expression level, signal-to-noise and other error terms such as the standard deviation and error.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. In this particular case we have highlighted and selected # 5 on this SEARCH RESULTS page. The annotation for this probe set mentions that it targets the last three exons and the 3Õ untranslated region (UTR) of the amyloid precursor protein (APP).<span style="mso-spacerun: yes"> </span>That is just what we want.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>3. Most probe sets have not been annotated in as much detail as App. Refer tot the FAQ to learn how to annotate probe sets yourself.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005.htm new file mode 100755 index 00000000..53f61532 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0005.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img border=0 src="slide0005_image013.png" style='position:absolute;top:8.83%; left:2.51%;width:77.48%;height:80.56%'> <div style='position:absolute;top:1.06%;left:0%;width:108.21%;height:8.3%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:56;position:absolute;top:0%;left:1.83%;width:98.16%; height:78.72%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>First page of data: The Trait Data and Analysis Form</span><span style='font-size:106%;color:#E9EB5D; mso-color-index:3;mso-special-format:lastCR;display:none'><br> </span></div> </div> <img border=0 src="slide0005_image014.png" style='position:absolute;top:34.98%; left:68.74%;width:16.42%;height:9.71%'> <div style='position:absolute;top:23.32%;left:84.76%;width:16.68%;height:34.09%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:2.07%;left:6.34%;width:93.65%; height:95.33%'><span style='position:absolute;top:0%;left:0%;width:90.67%'><span style='font-size:200%;color:#E9EB5D'><i>Click </i></span></span><span style='position:absolute;top:16.3%;left:0%;width:90.67%'><span style='font-size:200%;color:#E9EB5D'><i>here<br> </i></span></span> <div style='position:absolute;top:33.15%;left:0%;width:100.0%;height:16.84%'><span style='font-size:200%;color:#E9EB5D'><i>to learn<br> </i></span></div> <div style='position:absolute;top:49.45%;left:0%;width:90.67%;height:16.84%'><span style='font-size:200%;color:#E9EB5D'><i>about<br> </i></span></div> <div style='position:absolute;top:66.3%;left:0%;width:90.67%;height:16.84%'><span style='font-size:200%;color:#E9EB5D'><i>data<br> </i></span></div> <div style='position:absolute;top:83.15%;left:0%;width:90.67%;height:16.84%'><span style='font-size:200%;color:#E9EB5D'><i>source</i></span></div> </div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The Trait Data and Analysis Form is the single most important page from the point of view of working with GeneNetwork data. Please read the text carefully. Explore the links, but do not close this page. We will need it many more times in this demonstration.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. What is this database? It is called INIA Brain mRNA M430 (Apr05) PDNN, but what does that actually mean. How much of the brain was used? How were the animals processed? Most of these types of questions can be answered by clicking on the DATABASE link.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. Transcript/gene LOCATION data is usually from the most recent assembly. You can VERIFY the location of the probes and probe set using the two VERIFY buttons. VERIFY UCSC performs a sequence alignment (BLAT analysis) of the probes to the most recent assembly.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. The PROBE TOOL button provides you with highly detailed information on the probe sequences used to assemble the probe set. For example, in this case you can find out which probes correspond to which of the three exons. You can also review the performance of the individual probes. Please check the GLOSSARY for additional details on probes.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>4. The identifiers (IDs) provide links to other key resources.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image013.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image013.png new file mode 100755 index 00000000..55769e36 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image013.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image014.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image014.png new file mode 100755 index 00000000..e49ba16e --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image014.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_notes_pane.htm new file mode 100755 index 00000000..fbe8c631 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>The Trait Data and Analysis Form is the single most important page from the point of view of working with GeneNetwork data. Please read the text carefully. Explore the links, but do not close this page. We will need it many more times in this demonstration.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>1. What is this database? It is called INIA Brain mRNA M430 (Apr05) PDNN, but what does that actually mean. How much of the brain was used? How were the animals processed? Most of these types of questions can be answered by clicking on the DATABASE link.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. Transcript/gene LOCATION data is usually from the most recent assembly. You can VERIFY the location of the probes and probe set using the two VERIFY buttons. VERIFY UCSC performs a sequence alignment (BLAT analysis) of the probes to the most recent assembly.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>3. The PROBE TOOL button provides you with highly detailed information on the probe sequences used to assemble the probe set. For example, in this case you can find out which probes correspond to which of the three exons. You can also review the performance of the individual probes. Please check the GLOSSARY for additional details on probes.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>4. The identifiers (IDs) provide links to other key resources.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006.htm new file mode 100755 index 00000000..fa44d20c --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0006.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:-1.06%;left:0%;width:100.26%;height:10.07%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:56;position:absolute;top:0%;left:1.98%;width:96.82%; height:73.68%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Data sources: Metadata for each resource</span></div> </div> <img border=0 src="slide0006_image015.png" style='position:absolute;top:6.71%; left:3.31%;width:60.39%;height:92.22%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Most of the database components and resources in The GeneNetwork are linked to metadata pages that provide a human-readable summary of how, why, where, when, and with whom the data were generated. Before you get too involved with a data set, it is naturally important to read this information. While the data in The GeneNetwork may be accessible and useful, that does not always mean that the data is public domain and available for you to use in publication or for profit purposes. If you want to know more about the data ownership and usage, please read through the POLICIES pop-down menu items.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_image015.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_image015.png new file mode 100755 index 00000000..ff7d776a --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_image015.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_notes_pane.htm new file mode 100755 index 00000000..f29819ad --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Most of the database components and resources in The GeneNetwork are linked to metadata pages that provide a human-readable summary of how, why, where, when, and with whom the data were generated. Before you get too involved with a data set, it is naturally important to read this information. While the data in The GeneNetwork may be accessible and useful, that does not always mean that the data is public domain and available for you to use in publication or for profit purposes. If you want to know more about the data ownership and usage, please read through the POLICIES pop-down menu items.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007.htm new file mode 100755 index 00000000..a30b21f1 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0007.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:-.35%;left:-.79%;width:109.13%;height:7.42%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:56;position:absolute;top:0%;left:1.82%;width:98.17%; height:88.09%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Expression estimates for </span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'> on the Trait Data form</span><span style='font-size:81%;color:#E9EB5D;mso-color-index:3'> </span></div> </div> <div style='position:absolute;top:81.09%;left:2.51%;width:110.46%;height:11.48%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='position:absolute;top:7.69%;left:.83%;width:99.16%; height:84.61%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:183%;color:#E9EB5D;mso-color-index: 3'>Trait data for each strain with SE when known. For array data the scale is </span></span><span style='position:absolute;top:49.09%;left:0%;width:84.28%'><span style='font-family:"Gill Sans";font-size:183%;color:#E9EB5D;mso-color-index: 3'>~ log base 2.<span style="mso-spacerun: yes"> </span></span><span style='font-size:167%;color:#E9EB5D;mso-color-index:3'>F1 data = 16.723 = 2^16.723 = 108,174</span></span></div> </div> <img border=0 src="slide0007_image016.png" style='position:absolute;top:7.77%; left:2.51%;width:51.65%;height:72.26%'><img border=0 src="slide0007_image017.png" style='position:absolute;top:33.92%;left:57.88%; width:30.72%;height:13.42%'> <div style='position:absolute;top:47.7%;left:57.48%;width:36.29%;height:18.9%; filter:DropShadow(Color=#000000, OffX=2, OffY=1)'> <div class=O style='position:absolute;top:3.73%;left:2.91%;width:97.08%; height:96.26%'><span style='position:absolute;top:0%;left:0%;width:96.24%'><span style='font-size:167%;color:#E9EB5D;mso-color-index:3'>These values can all </span></span><span style='position:absolute;top:25.24%;left:0%;width:93.98%'><span style='font-size:167%;color:#E9EB5D;mso-color-index:3'>be changed by the </span></span><span style='position:absolute;top:49.51%;left:0%;width:100.0%'><span style='font-size:167%;color:#E9EB5D;mso-color-index:3'>user. (Yes, there is a </span></span><span style='position:absolute;top:74.75%;left:0%;width:93.98%'><span style='font-size:167%;color:#E9EB5D;mso-color-index:3'>RESET)</span></span></div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>This slide shows you the lower parts of the Trait Data and Analysis Form with the data for the first set of BXD strains</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_image016.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_image016.png new file mode 100755 index 00000000..53a17c76 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_image016.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_image017.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_image017.png new file mode 100755 index 00000000..308c4df0 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_image017.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_notes_pane.htm new file mode 100755 index 00000000..f5bc813e --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>This slide shows you the lower parts of the Trait Data and Analysis Form with the data for the first set of BXD strains</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008.htm new file mode 100755 index 00000000..c0fa9166 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0008.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:.53%;left:.79%;width:98.54%;height:8.12%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:56;position:absolute;top:0%;left:2.01%;width:96.9%; height:91.3%'><span style='mso-special-format:nobullet;display:none;color:#FBFDB8; font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size: 106%;color:#E9EB5D;mso-color-index:3'>Critiquing the </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> data the Trait Data</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </div> <div style='position:absolute;top:74.38%;left:2.51%;width:110.86%;height:13.78%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='position:absolute;top:6.41%;left:.83%;width:99.16%; height:88.46%'><span style='position:absolute;top:0%;left:0%;width:98.55%'><span style='font-family:"Gill Sans";font-size:150%;color:#E9EB5D;mso-color-index: 3'>Use the BASIC STATISTICS button to evaluate the App data. You will find that App data </span></span><span style='position:absolute;top:31.88%;left:0%; width:100.0%'><span style='font-family:"Gill Sans";font-size:150%;color:#E9EB5D; mso-color-index:3'>from the different strains are not equally trustworthy. BXD8 is an obvious outlier without </span></span><span style='position:absolute; top:63.76%;left:0%;width:93.85%'><span style='font-family:"Gill Sans"; font-size:150%;color:#E9EB5D;mso-color-index:3'>replication (no error bar)</span><span style='font-size:150%;color:#E9EB5D;mso-color-index:3'>. BXD33 is also suspiciously low. BXD5 is noisy. </span><span style='font-family:"Gill Sans"; font-size:150%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></span></div> </div> <img border=0 src="slide0008_image018.png" style='position:absolute;top:7.77%; left:2.11%;width:16.02%;height:18.72%'><img border=0 src="slide0008_image019.png" style='position:absolute;top:8.3%;left:18.27%; width:73.37%;height:66.07%'><img border=0 src="slide0008_image021.png" style='position:absolute;top:87.27%;left:59.6%;width:30.72%;height:13.42%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The Basic Statistics page allows you to evaluate some aspects of the data quality. In this case, BXD8 is a potential problem. An outlier of this type may be generated by a technical artifact (bad sample?). However, it is also possible that BXD8 just has genuine low endogenous expression of App and may therefore be a particularly valuable model for research. There are different ways to treat problematic data of these types. One way is simply to discard this datum. The other way is to prevent outliers from have too much influence quantitatively, while leaving them in their low (or high positions). This is called windsorizing the data (after King Henry the VIII who had a habit of chopping heads). In this case, we have windsorized the BXD8 to a value of 16.0 and the BXD33 to a value of 16.02. Rank is retained. We are making a bet that the two lowest strains are really low, but we are hedging our bet and just making them a little lower than BXD90. This removes their ÒundueÓ influence.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. It turns out that BXD8 is a strain with many odd phenotypes. The whole strain is essentially an outlier for many traits. Therefore, the low App expression data may be quite accurate. Still, it would be comforting to have at least two more replicates.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image018.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image018.png new file mode 100755 index 00000000..9535e6bb --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image018.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image019.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image019.png new file mode 100755 index 00000000..7e86d735 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image019.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image021.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image021.png new file mode 100755 index 00000000..2f8dfb0a --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image021.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_notes_pane.htm new file mode 100755 index 00000000..455928c7 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>The Basic Statistics page allows you to evaluate some aspects of the data quality. In this case, BXD8 is a potential problem. An outlier of this type may be generated by a technical artifact (bad sample?). However, it is also possible that BXD8 just has genuine low endogenous expression of App and may therefore be a particularly valuable model for research. There are different ways to treat problematic data of these types. One way is simply to discard this datum. The other way is to prevent outliers from have too much influence quantitatively, while leaving them in their low (or high positions). This is called windsorizing the data (after King Henry the VIII who had a habit of chopping heads). In this case, we have windsorized the BXD8 to a value of 16.0 and the BXD33 to a value of 16.02. Rank is retained. We are making a bet that the two lowest strains are really low, but we are hedging our bet and just making them a little lower than BXD90. This removes their ÒundueÓ influence.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>1. It turns out that BXD8 is a strain with many odd phenotypes. The whole strain is essentially an outlier for many traits. Therefore, the low App expression data may be quite accurate. Still, it would be comforting to have at least two more replicates.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009.htm new file mode 100755 index 00000000..2daff7ac --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0009.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:0%;left:1.72%;width:93.64%;height:14.48%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:56;position:absolute;top:0%;left:2.12%;width:96.6%; height:51.21%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> expression after windsorizing</span></div> </div> <img border=0 src="slide0009_image022.png" style='position:absolute;top:8.83%; left:2.51%;width:94.17%;height:83.74%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Now we get a much better feel for the variation in the error among the cases. Those without error bars are of course the ÒnoisiestÓ of all. This data set is not complete yet (the aim is to acquire at least one male-female sample for each BXD strain).</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009_image022.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009_image022.png new file mode 100755 index 00000000..e03c35ed --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009_image022.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009_notes_pane.htm new file mode 100755 index 00000000..b2f9f9f2 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Now we get a much better feel for the variation in the error among the cases. Those without error bars are of course the ÒnoisiestÓ of all. This data set is not complete yet (the aim is to acquire at least one male-female sample for each BXD strain).</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010.htm new file mode 100755 index 00000000..4d02c34e --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0010.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:0%;left:.79%;width:93.64%;height:14.48%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:56;position:absolute;top:0%;left:2.12%;width:97.45%; height:51.21%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Discovering shared expression patterns</span></div> </div> <img border=0 src="slide0010_image023.png" style='position:absolute;top:10.07%; left:3.31%;width:94.17%;height:37.27%'><img border=0 src="slide0010_image024.png" style='position:absolute;top:38.86%;left:61.72%; width:13.77%;height:14.84%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Finally, we can now start an analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>We ask a simple question:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Do differences in this particular App transcript steady-state abundance level correlate with those of any other transcripts in the same INIA Brain mRNA M430 data set?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Helvetica size=3>You can CHOOSE many other DATABASES at this point if you want, but for now letÕs stick with the default.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. There are different ways to sort the correlations. The most obvious is by p-value (most significant values at the top of the list), but it is also interesting to sort the top 100 or top 500 by their gene symbol (gene ID) or by their chromosomal location (position).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. If you donÕt want your analysis to be sensitive to outliers, then you may want to choose to use the Spearman Rank Order method of calculating correlations.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_image023.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_image023.png new file mode 100755 index 00000000..1d32d035 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_image023.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_image024.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_image024.png new file mode 100755 index 00000000..152e5045 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_image024.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_notes_pane.htm new file mode 100755 index 00000000..3d3f0e48 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Finally, we can now start an analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>We ask a simple question:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Do differences in this particular App transcript steady-state abundance level correlate with those of any other transcripts in the same INIA Brain mRNA M430 data set?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Helvetica size=2>You can CHOOSE many other DATABASES at this point if you want, but for now letÕs stick with the default.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. There are different ways to sort the correlations. The most obvious is by p-value (most significant values at the top of the list), but it is also interesting to sort the top 100 or top 500 by their gene symbol (gene ID) or by their chromosomal location (position).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>3. If you donÕt want your analysis to be sensitive to outliers, then you may want to choose to use the Spearman Rank Order method of calculating correlations.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011.htm new file mode 100755 index 00000000..362057fc --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0011.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:.35%;left:-.79%;width:93.64%;height:14.48%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:56;position:absolute;top:0%;left:2.12%;width:96.6%; height:51.21%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Transcript neighborhoods</span></div> </div> <img border=0 src="slide0011_image025.png" style='position:absolute;top:7.77%; left:2.51%;width:85.82%;height:91.87%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The Traits Correlation output window (Correlation Results) compares App expression data with all other traits in this INIA Brain data set. The most significant 100 or 500 transcripts are sorted by their p-values. The top correlation is that of the probe set to itself (often a value of 1.0, but in this case we modified the App values manually by windsorizing the data). The next best correlation is to another App probe set. The fourth correlation is interesting and suggests that there may be a link between App and a particular type of ataxia (Atcay).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Helvetica size=3>Use the checkboxes to the far left to select traits that you want to study together. Once you have selected interesting traits, click on the ADD SELECTION button. This puts all of the selected traits into a SELECTIONS WINDOW for other types of analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. The p-value is not corrected for multiple tests. A conservative approach for array data would be to assume 10,000 nominally independent tests. Subtract 4 from the exponent and if the value is still smaller than 0.05 you may have a real correlation.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. The LITERATURE CORRELATION is a data type generated by Drs. Ramin Homayouni and Michael Berry. Click on the header column by the asterisk for more information on this highly useful data type.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>4. We are using Pearson product moment correlations rather that the Spearman rank order correlation. But you can select either in the previous step.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011_image025.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011_image025.png new file mode 100755 index 00000000..d29a333f --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011_image025.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011_notes_pane.htm new file mode 100755 index 00000000..1f0dd0d1 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>The Traits Correlation output window (Correlation Results) compares App expression data with all other traits in this INIA Brain data set. The most significant 100 or 500 transcripts are sorted by their p-values. The top correlation is that of the probe set to itself (often a value of 1.0, but in this case we modified the App values manually by windsorizing the data). The next best correlation is to another App probe set. The fourth correlation is interesting and suggests that there may be a link between App and a particular type of ataxia (Atcay).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Helvetica size=2>Use the checkboxes to the far left to select traits that you want to study together. Once you have selected interesting traits, click on the ADD SELECTION button. This puts all of the selected traits into a SELECTIONS WINDOW for other types of analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. The p-value is not corrected for multiple tests. A conservative approach for array data would be to assume 10,000 nominally independent tests. Subtract 4 from the exponent and if the value is still smaller than 0.05 you may have a real correlation.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>3. The LITERATURE CORRELATION is a data type generated by Drs. Ramin Homayouni and Michael Berry. Click on the header column by the asterisk for more information on this highly useful data type.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>4. We are using Pearson product moment correlations rather that the Spearman rank order correlation. But you can select either in the previous step.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012.htm new file mode 100755 index 00000000..4f1cf425 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0012.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:.35%;left:1.72%;width:93.64%;height:14.48%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:56;position:absolute;top:0%;left:2.12%;width:96.6%; height:51.21%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> and </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>Atcay</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> transcript scatterplot </span></div> </div> <img border=0 src="slide0012_image026.png" style='position:absolute;top:8.48%; left:5.03%;width:66.22%;height:91.16%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>By clicking on the CORRELATION of the Atcay transcript to the App transcript, you can generate a Correlation plot between these two transcripts. In this App and Atcay scatterplot, each point is a strain mean value. For example, BXD33 and BXD8 have low App and Atcay expressions. The two parental strains and the F1 are also included in this plot.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012_image026.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012_image026.png new file mode 100755 index 00000000..a0675ffc --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012_image026.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012_notes_pane.htm new file mode 100755 index 00000000..c13d07ec --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>By clicking on the CORRELATION of the Atcay transcript to the App transcript, you can generate a Correlation plot between these two transcripts. In this App and Atcay scatterplot, each point is a strain mean value. For example, BXD33 and BXD8 have low App and Atcay expressions. The two parental strains and the F1 are also included in this plot.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013.htm new file mode 100755 index 00000000..5aa623bf --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0013.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:.35%;left:.79%;width:99.47%;height:14.48%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:56;position:absolute;top:0%;left:1.99%;width:96.8%; height:51.21%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> transcript and eight of its neighbors</span></div> </div> <img border=0 src="slide0013_image027.png" style='position:absolute;top:9.71%; left:2.51%;width:83.84%;height:90.1%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>A group of traits from many different databases can be selected and brought together for joint analysis. In this case all of the content of the BXD SELECTIONS is from a single BRAIN database, the top 20 neighbors of the App transcript from the Correlation Results table. Eight of these neighbors plus App is shown in the slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Helvetica size=3>All of items in the BXD SELECTIONS were selected using the SELECT ALL button</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. The buttons at the top (and bottom) of this page can do some cool stuff. We will work with NETWORK GRAPH first.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. Think of the SELECTIONS as your shopping cart. You go to different aisles in the supermarket to acquire different types of items of interest. These could include transcripts, classical phenotypes (longevity, brain weight, prepulse inhibition, iron levels in midbrain). ÒChecking outÓ in this case involves doing some analysis with the items in the cart.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>4. Different tools handle different numbers of items. Most will handle up to 100 traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_image027.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_image027.png new file mode 100755 index 00000000..ba473846 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_image027.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_notes_pane.htm new file mode 100755 index 00000000..4d56b194 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>A group of traits from many different databases can be selected and brought together for joint analysis. In this case all of the content of the BXD SELECTIONS is from a single BRAIN database, the top 20 neighbors of the App transcript from the Correlation Results table. Eight of these neighbors plus App is shown in the slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Helvetica size=2>All of items in the BXD SELECTIONS were selected using the SELECT ALL button</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. The buttons at the top (and bottom) of this page can do some cool stuff. We will work with NETWORK GRAPH first.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>3. Think of the SELECTIONS as your shopping cart. You go to different aisles in the supermarket to acquire different types of items of interest. These could include transcripts, classical phenotypes (longevity, brain weight, prepulse inhibition, iron levels in midbrain). ÒChecking outÓ in this case involves doing some analysis with the items in the cart.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>4. Different tools handle different numbers of items. Most will handle up to 100 traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014.htm new file mode 100755 index 00000000..156a5132 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: App transcript coexpression neighborhood"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0014.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:82.15%;left:4.1%;width:96.15%;height:18.19%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'></div> <div style='position:absolute;top:-2.29%;left:.79%;width:105.43%;height:12.54%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='position:absolute;top:19.71%;left:1.25%;width:98.74%; height:61.97%'><span style='font-size:82%'><i>App</i></span><span style='font-size:82%'> transcript coexpression neighborhood</span><span style='mso-special-format:lastCR;display:none'><br> </span></div> </div> <img border=0 src="slide0014_image029.png" style='position:absolute;top:37.8%; left:1.72%;width:97.48%;height:62.19%'><img border=0 src="slide0014_image031.png" style='position:absolute;top:11.13%;left:1.72%; width:79.47%;height:25.44%'><img border=0 src="slide0014_image033.png" style='position:absolute;top:10.6%;left:81.32%;width:18.8%;height:9.89%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Output of the Network Graph. Warm colors (orange and red) are positive correlations above 0.5 whereas cool colors (green and blue) are negative correlations. Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Helvetica size=3> All of the nodes (gene/transcripts) on this graph are clickable.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. For this graph the App expression values have ÒrevertedÓ to their pre-Windsorized values.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. To generate this graph, we used the default setting:<span style="mso-spacerun: yes"> </span>Size of 16 by 16 inches; Gene Symbols; Don't Show Correlations; Use curved lines (aka ÒedgesÓ).</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image029.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image029.png new file mode 100755 index 00000000..8f560834 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image029.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image031.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image031.png new file mode 100755 index 00000000..8d72b4c1 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image031.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image033.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image033.png new file mode 100755 index 00000000..c1cd1c01 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image033.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_notes_pane.htm new file mode 100755 index 00000000..728a1a82 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Output of the Network Graph. Warm colors (orange and red) are positive correlations above 0.5 whereas cool colors (green and blue) are negative correlations. Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Helvetica size=2> All of the nodes (gene/transcripts) on this graph are clickable.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. For this graph the App expression values have ÒrevertedÓ to their pre-Windsorized values.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>3. To generate this graph, we used the default setting:<span style="mso-spacerun: yes"> </span>Size of 16 by 16 inches; Gene Symbols; Don't Show Correlations; Use curved lines (aka ÒedgesÓ).</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015.htm new file mode 100755 index 00000000..c2a26be3 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0015.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:0%;left:.79%;width:93.64%;height:14.48%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:292; mso-text-indent-alt:0;position:absolute;top:0%;left:1.13%;width:97.59%; height:51.21%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Correlations of </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> with classical traits</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </div> <img border=0 src="slide0015_image034.png" style='position:absolute;top:28.97%; left:4.1%;width:78.27%;height:70.84%'><img border=0 src="slide0015_image035.png" style='position:absolute;top:8.12%;left:4.1%;width:33.5%;height:19.61%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Going back to the Trait Data and Analysis Form window, we have computed the correlations between strain variation in App expression level and other classical phenotypes that have already been measured in many of the same BXD strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Helvetica size=3>The number of common strains varies widely--in this case from 14 to 23 strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. We can add these traits (four are selected) to our BXD SELECTIONS window.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_image034.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_image034.png new file mode 100755 index 00000000..dafa2898 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_image034.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_image035.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_image035.png new file mode 100755 index 00000000..35566d47 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_image035.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_notes_pane.htm new file mode 100755 index 00000000..373646fe --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Going back to the Trait Data and Analysis Form window, we have computed the correlations between strain variation in App expression level and other classical phenotypes that have already been measured in many of the same BXD strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Helvetica size=2>The number of common strains varies widely--in this case from 14 to 23 strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. We can add these traits (four are selected) to our BXD SELECTIONS window.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016.htm new file mode 100755 index 00000000..9432ca4c --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0016.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:0%;left:.79%;width:99.47%;height:10.24%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:292; mso-text-indent-alt:0;position:absolute;top:0%;left:1.06%;width:98.66%; height:72.41%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Network Graph of </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> with classical traits</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </div> <img border=0 src="slide0016_image036.png" style='position:absolute;top:8.3%; left:3.31%;width:88.21%;height:90.63%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>We have computed the Network Graph, now using other types of traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Saline Hot Plate Latency is the green node labeled 10020.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Freezing (fear) is the green node labeled 10447.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016_image036.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016_image036.png new file mode 100755 index 00000000..baa1d807 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016_image036.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016_notes_pane.htm new file mode 100755 index 00000000..c2a078c5 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>We have computed the Network Graph, now using other types of traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Saline Hot Plate Latency is the green node labeled 10020.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Freezing (fear) is the green node labeled 10447.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0017.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0017.htm new file mode 100755 index 00000000..afb498b8 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0017.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0017.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:1.41%;left:3.31%;width:93.64%;height:14.48%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:292; mso-text-indent-alt:0;position:absolute;top:0%;left:1.13%;width:97.59%; height:51.21%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Summary of Part 1:</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </div> <div style='position:absolute;top:10.77%;left:8.47%;width:100.79%;height:47.87%'> <div class=O1 style='mso-margin-left-alt:432'></div> <div class=O2 style='mso-margin-left-alt:720'></div> <div class=O3 style='mso-margin-left-alt:1008'></div> <div class=O4 style='mso-margin-left-alt:1296'></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:0%; left:0%;width:90.14%;height:11.07%'><span style='position:absolute;top:0%; left:2.76%;width:97.23%'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.84%;font-family:Arial'>1.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You have learned the basics about searching for traits<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:11.43%; left:0%;width:84.88%;height:11.07%'><span style='position:absolute;top:0%; left:2.94%;width:97.05%'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-3.03%;font-family:Arial'>2.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know some methods to check data quality<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:22.5%; left:0%;width:84.88%;height:11.07%'><span style='position:absolute;top:0%; left:2.94%;width:97.05%'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-3.03%;font-family:Arial'>3.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to edit bad or suspicious data<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:33.57%; left:0%;width:90.01%;height:11.07%'><span style='position:absolute;top:0%; left:2.77%;width:97.22%'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.85%;font-family:Arial'>4.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to review the basic statistics of a trait<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:44.64%; left:0%;width:93.56%;height:22.14%'><span style='position:absolute;top:0%; left:2.66%;width:97.33%'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.74%;font-family:Arial'>5.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to generate a scattergram between two </span></span><span style='position:absolute; top:50.0%;left:2.66%;width:88.06%'><span style='font-family:"Gill Sans"; font-size:200%;color:#E9EB5D;mso-color-index:3'>traits using the Traits Correlation tool<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:66.78%; left:0%;width:100.0%;height:11.07%'><span style='position:absolute;top:0%; left:2.49%;width:97.5%'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.56%;font-family:Arial'>6.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to add items to your SELECTIONS window<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:77.85%; left:0%;width:99.34%;height:22.14%'><span style='position:absolute;top:0%; left:2.51%;width:97.48%'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.57%;font-family:Arial'>7.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to generate a Network Graph of traits that </span></span><span style='position:absolute; top:51.66%;left:2.51%;width:82.93%'><span style='font-family:"Gill Sans"; font-size:200%;color:#E9EB5D;mso-color-index:3'>co-vary. </span></span></div> </div> <div class=O style='position:absolute;top:67.31%;left:5.96%;width:105.29%; height:26.5%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'>What does genetic covariance mean? The genetic covariance can </span></span><span style='position:absolute;top:20.0%;left:0%;width:96.1%'><span style='font-family: "Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:3'>be functional and mechanistic, but it can also be due to linkage </span></span><span style='position:absolute;top:40.0%;left:0%;width:95.97%'><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'>disequilibrium. Finally, it can be due to sampling error or poor </span></span><span style='position:absolute;top:60.66%;left:0%;width:87.92%'><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'>experimental design. Evaluate the biological plausibility of </span></span><span style='position:absolute;top:80.66%;left:0%;width:85.28%'><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'>correlations. Test and be skeptical.</span></span></div> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018.htm new file mode 100755 index 00000000..e1ee283b --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018.htm @@ -0,0 +1,25 @@ +<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Contact for comments and improvements:"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- +gId="slide0018.htm" +if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { + parent.base.g_done = 1; + document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); +} +if( !IsNts() ) Redirect( "PPTSld", gId ); +var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; +//--> +</script><script for=window event=onload language=JavaScript><!-- +if( !IsSldOrNts() ) return; +if( MakeNotesVis() ) return; +LoadSld( gId ); +playList();MakeSldVis(1); +//--> +</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:2.29%;left:2.51%;width:94.43%;height:9.89%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-358 0 -1";position:absolute;top:19.64%; left:1.4%;width:97.47%;height:69.64%'><span style='font-size:73%'><i>Contact for comments and improvements:</i></span><span style='font-size:82%;mso-special-format: lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:16.6%;left:6.62%;width:90.19%;height:24.38%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-358 0 -1";position:absolute;top:0%; left:1.46%;width:97.35%;height:100.0%'><span style='position:absolute; top:0%;left:0%;width:100.0%'><span style='font-size:82%'>rwilliam@nb.utmem.edu<br> </span></span><span style='position:absolute;top:34.05%;left:4.67%;width:95.47%'><span style='font-size:82%'><br> </span></span><span style='position:absolute; top:68.11%;left:4.67%;width:95.47%'><span style='font-size:82%;mso-special-format: lastCR;display:none'><br> </span></span></div> </div> <div class=O style='position:absolute;top:27.56%;left:9.4%;width:50.59%; height:7.77%'><span style='font-family:"Gill Sans";font-size:300%;color:#E9EB5D'>kmanly@utmem.edu</span></div> <div class=O style='position:absolute;top:83.56%;left:4.37%;width:108.34%; height:15.9%'><span style='position:absolute;top:0%;left:0%;width:90.83%'><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D'>The </span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D'><i>App</i></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D'> findings reviewed in this presentation are part of an </span></span><span style='position:absolute; top:33.33%;left:0%;width:100.0%'><span style='font-family:"Gill Sans"; font-size:200%;color:#E9EB5D'>ongoing study by R. Williams. R. Homayouni, and R. Clark (July 15, </span></span><span style='position:absolute;top:66.66%; left:0%;width:84.35%'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'>2005)</span><span style='font-family:"Gill Sans";font-size:300%; color:#E9EB5D;mso-special-format:lastCR;display:none'><br> </span></span></div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>END</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_image037.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_image037.png new file mode 100755 index 00000000..a1cb20e4 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_image037.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_image038.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_image038.png new file mode 100755 index 00000000..e06bd0db --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_image038.png Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_notes_pane.htm new file mode 100755 index 00000000..e2cb435a --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>END</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0019.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0019.htm new file mode 100755 index 00000000..e6b8658d --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0019.htm @@ -0,0 +1,153 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: GeneNetwork and WebQTL:"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0019.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.03 * g_width; myheight = 0.09 * g_height; mywidth = 0.84 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.09 * g_height; mywidth = 0.82 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-277 0 -1";mso-margin-left-alt:232; mso-text-indent-alt:0;mso-line-spacing:"-277 0 -1";mso-margin-left-alt:232; mso-text-indent-alt:0'><span style='font-size:105%'><i>GeneNetwork and WebQTL:</i></span><span style='font-size:68%;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> + mytop = 0.24 * g_height; myleft = 0.05 * g_width; myheight = 0.5 * g_height; mywidth = 0.69 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.36 * g_height; mywidth = 0.67 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.19 * g_height; mywidth = 0.62 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-256 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.62 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Part 1: How to study </span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0.05 * g_width; myheight = 0.07 * g_height; mywidth = 0.57 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>expression variation and </span></span></layer><script> + mytop = 0.11 * g_height; myleft = 0.05 * g_width; myheight = 0.07 * g_height; mywidth = 0.57 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>covariation (slides 2–16)<br> </span></span></layer></div> </layer><script> + mytop = 0.22 * g_height; myleft = 0 * g_width; myheight = 0.13 * g_height; mywidth = 0.67 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-256 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.67 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Part 2. Discovering upstream </span></span></layer><script> + mytop = 0.06 * g_height; myleft = 0.05 * g_width; myheight = 0.07 * g_height; mywidth = 0.59 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>modulators (slides 17–30)</span><span style='font-size:94%;color:#E9EB5D; mso-color-index:3;mso-special-format:lastCR;display:none'><br> </span></span></layer></div> </layer></div> </layer></div> </layer><script> + mytop = 0.21 * g_height; myleft = 0.74 * g_width; myheight = 0.64 * g_height; mywidth = 0.23 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.74 * g_width; +yy = 0.21 * g_height; +ht = 0.64 * g_height; +wd = 0.23 * g_width; +document.write( +'<img border=0 src="slide0001_image001.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.79 * g_height; myleft = 0.75 * g_width; myheight = 0.14 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:"Arial Rounded MT Bold";font-size:233%;color:#6E6E6E'>RNA</span><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; display:none'><br> </span></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.66 * g_height; myleft = 0.03 * g_width; myheight = 0.11 * g_height; mywidth = 0.8 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.8 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'><i>PowerPoint ÒNormal viewÓ has notes that may be </i></span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.69 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'><i>useful companions to these slides.</i></span><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3;mso-special-format:lastCR;display:none'><br> </span></span></layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.06 * g_width; myheight = 0.07 * g_height; mywidth = 0.55 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:283%; color:#E9EB5D'><i>a PowerPoint Presentation</i></span><span style='font-family: "Gill Sans";font-size:317%;color:#E9EB5D;mso-special-format:lastCR;display: none'><i><br> </i></span></div> </layer><script> + mytop = 0.92 * g_height; myleft = 0.75 * g_width; myheight = 0.03 * g_height; mywidth = 0.26 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:Helvetica;font-size:167%; color:#E9EB5D'><i>RWW 07.23.2005</i></span></div> </layer><script> + mytop = 0.81 * g_height; myleft = 0.03 * g_width; myheight = 0.11 * g_height; mywidth = 0.77 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.68 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'><i>You can also download this PowerPoint at<br> </i></span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.77 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'><i>ftp://atlas.utmem.edu/public/webqtl_demo2.ppt </i></span><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Welcome to a short demonstration of the GeneNetwork and its WebQTL module. Please adjust the size of the windows on your monitor so that you can see part of this page, as well as GeneNetwork windows. WebQTL produces a large number of new windows, so you may need to modify your browser preferences to permit pop-ups. In this demonstration, we explore one important transcript expressed in the brain: the amyloid beta precursor protein messenger RNA. A protein product of this mRNA, the APP protein, is associated with AlzheimerÕs disease.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>My thanks to Dr. Robert F. Clark and Wenli Cai for testing this PowerPoint demonstration and making many improvements.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>(Initial version of June 2003 by Rob Williams. Edits July 13, 2005 by RW and RFC. Edit July 14, 2005 by WC. Final edits by RF Clark, July 22, 2005.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0019_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0019_notes_pane.htm new file mode 100755 index 00000000..e2cb435a --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0019_notes_pane.htm @@ -0,0 +1,5 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>END</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0020.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0020.htm new file mode 100755 index 00000000..da8b9759 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0020.htm @@ -0,0 +1,172 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0020.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.86 * g_height; mywidth = 0.86 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0 * g_width; +yy = 0.08 * g_height; +ht = 0.86 * g_height; +wd = 0.86 * g_width; +document.write( +'<img border=0 src="slide0002_image002.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.34 * g_height; myleft = 0.59 * g_width; myheight = 0.14 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.59 * g_width; +yy = 0.34 * g_height; +ht = 0.14 * g_height; +wd = 0.12 * g_width; +document.write( +'<img border=0 src="slide0002_image003.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.46 * g_height; myleft = 0.85 * g_width; myheight = 0.12 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-224 0 0"'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'>Choose<br> </span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-224 0 0"'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'>database</span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.62 * g_height; myleft = 0.86 * g_width; myheight = 0.12 * g_height; mywidth = 0.21 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'>Enter<br> </span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-224 0 0"'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'><i>APP</i></span><span style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D;mso-color-index: 3;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.77 * g_height; myleft = 0.85 * g_width; myheight = 0.12 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'>Select<br> </span></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-224 0 0"'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'>search</span></div> </layer></div> </layer></div> </layer><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.09 * g_height; mywidth = 1.11 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div> <layer> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'></div> </layer> <script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 1.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:0'><span style='mso-special-format:nobullet;display: none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>PART 1: How to study variation and covariation</span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.15 * g_height; myleft = 0.85 * g_width; myheight = 0.22 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.21 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:"-224 0 0";mso-line-spacing:"-224 0 0"'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>Choose<span style="mso-spacerun: yes"> </span></span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>species, </span></span></layer><script> + mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>group, </span></span></layer><script> + mytop = 0.15 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>and type</span></span></layer></div> </layer></div> </layer><script> + mytop = 0.71 * g_height; myleft = 0.48 * g_width; myheight = 0.13 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.48 * g_width; +yy = 0.71 * g_height; +ht = 0.13 * g_height; +wd = 0.12 * g_width; +document.write( +'<img border=0 src="slide0002_image004.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Please link to the web site:<span style="mso-spacerun: yes"> </span>http://www.genenetwork.org</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>To begin a search you make choices about what species, group, and database to explore.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>For this demonstration enter APP as above and click on the SEARCH button. Make sure that the DEFAULT SETTINGS are species = Mouse, Group = BXD, Type = Whole Brain, and Database = INIA BRAIN mRNA M430 (Apr05) PDNN.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. The GeneNetwork and WebQTL are often used to work with public data sets. However, it is possible to enter and analyze your own data for specific genetic reference populations such as the BXD genetic reference population of mice or the HXB strains of rat. Entering your own data is a more advanced topic, but if you click on the HOME pop-down menu (upper left), you will see ÒEnter Trait DataÓ that will explain the process.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>2.</font><font face=Helvetica size=3> For help on advanced searching methods read the left side of the page (INTRODUCTION).<span style="mso-spacerun: yes"> </span>If you make a search term too complex, you may get no hits (try entering Òamyloid betaÓ for example). If you make it too simple, you may also get too many.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>3.</font><font face=Helvetica size=3> Use the asterisk * as a wildcard. For example, to find all <i>Hoxb</i> transcripts, search for Hoxb*.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>4.</font><font face=Helvetica size=3> In some cases you can also research for transcripts and genes using special search strings such as Ò</font><font face=Geneva size=3>Mb = (Chr1, 100 102)Ó to find all genes on Chromosome 1 between 98 and 104 megabases (donÕt actually use the quotes). Details are described at </font><font face=Verdana size=3>http://www.genenetwork.org/searchHelp.html</font><font face=Geneva size=3>.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>5.<span style="mso-spacerun: yes"> </span>These INFO buttons provide links to data about the different data types. Try them.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>6.<span style="mso-spacerun: yes"> </span>The SET TO DEFAULT button is used to change the database default setting to match your typical search categories.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0021.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0021.htm new file mode 100755 index 00000000..0e0eb529 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0021.htm @@ -0,0 +1,129 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0021.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.34 * g_height; myleft = 0.59 * g_width; myheight = 0.14 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.59 * g_width; +yy = 0.34 * g_height; +ht = 0.14 * g_height; +wd = 0.12 * g_width; +document.write( +'<img border=0 src="slide0003_image005.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.09 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div> <layer> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'></div> </layer> <script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 1.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:0'><span style='mso-special-format:nobullet;display: none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Please also use the Glossary, FAQ, and News</span></div> </layer></div> </layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.01 * g_width; myheight = 0.6 * g_height; mywidth = 0.69 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.1 * g_height; +ht = 0.6 * g_height; +wd = 0.69 * g_width; +document.write( +'<img border=0 src="slide0003_image006.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.09 * g_height; myleft = 0.18 * g_width; myheight = 0.13 * g_height; mywidth = 0.12 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.18 * g_width; +yy = 0.09 * g_height; +ht = 0.13 * g_height; +wd = 0.12 * g_width; +document.write( +'<img border=0 src="slide0003_image008.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.49 * g_height; myleft = 0.38 * g_width; myheight = 0.48 * g_height; mywidth = 0.6 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.38 * g_width; +yy = 0.49 * g_height; +ht = 0.48 * g_height; +wd = 0.6 * g_width; +document.write( +'<img border=0 src="slide0003_image009.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>SHORT DETOUR to the HELP menu. If you are new to the GeneNetwork, you may find it helpful to review the The Glossary and FAQ pages shown above. We are in the process of making ÒliveÓ demos for some of the key modules in the GeneNetwork. Check the NEWS every month or two to find out about new features.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0022.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0022.htm new file mode 100755 index 00000000..663a5f0f --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0022.htm @@ -0,0 +1,140 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Search results"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0022.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.09 * g_height; myleft = 0.03 * g_width; myheight = 0.9 * g_height; mywidth = 0.68 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.03 * g_width; +yy = 0.09 * g_height; +ht = 0.9 * g_height; +wd = 0.68 * g_width; +document.write( +'<img border=0 src="slide0004_image010.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.63 * g_height; myleft = 0.63 * g_width; myheight = 0.06 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.63 * g_width; +yy = 0.63 * g_height; +ht = 0.06 * g_height; +wd = 0.14 * g_width; +document.write( +'<img border=0 src="slide0004_image012.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.45 * g_height; myleft = 0.8 * g_width; myheight = 0.47 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.21 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-224 0 0"'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>Highlight </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>this probe </span></span></layer><script> + mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>set in red </span></span></layer><script> + mytop = 0.15 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>and</span><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3;display:none'><i><br> </i></span></span></layer></div> </layer><script> + mytop = 0.2 * g_height; myleft = 0 * g_width; myheight = 0.26 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-line-spacing:"-224 0 0"'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>click. You </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>do NOT </span></span></layer><script> + mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>have to </span></span></layer><script> + mytop = 0.15 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>select the </span></span></layer><script> + mytop = 0.2 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>checkbox</span><span style='font-family:"Gill Sans"; font-size:250%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></span></layer></div> </layer></div> </layer><script> + mytop = -0.04 * g_height; myleft = 0.01 * g_width; myheight = 0.18 * g_height; mywidth = 0.84 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.05 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.82 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%'><span style='font-size:82%'>Search results</span><span style='mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>RESULTS OF THE APP SEARCH.<span style="mso-spacerun: yes"> </span>A search of the INIA Brain database generates 18 matches, 10 of which are shown above. The GeneNetwork will display several hundred matches in pages of 40 each. If a search generates a larger numbers of hits, then you will need to refine search terms.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. APP is a great transcript to introduce you to the complexity and power of new array platforms that often provide ÒalternativeÓ expression estimates for single genes. There are seven probe sets that target different parts of the APP transcript. Which of the alternative measurements is most appropriate and informative? Have a look at the FAQ page for more on this topic, but general advice: 1. be skeptical and try to validate that the correct transcript and gene is being measured; 2. check what part of the transcript is complementary to the probes; 3. evaluate the performance of individual probes based on expression level, signal-to-noise and other error terms such as the standard deviation and error.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. In this particular case we have highlighted and selected # 5 on this SEARCH RESULTS page. The annotation for this probe set mentions that it targets the last three exons and the 3Õ untranslated region (UTR) of the amyloid precursor protein (APP).<span style="mso-spacerun: yes"> </span>That is just what we want.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. Most probe sets have not been annotated in as much detail as App. Refer tot the FAQ to learn how to annotate probe sets yourself.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0023.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0023.htm new file mode 100755 index 00000000..10a6218a --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0023.htm @@ -0,0 +1,128 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0023.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0.02 * g_width; myheight = 0.8 * g_height; mywidth = 0.77 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.02 * g_width; +yy = 0.08 * g_height; +ht = 0.8 * g_height; +wd = 0.77 * g_width; +document.write( +'<img border=0 src="slide0005_image013.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 1.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 1.06 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56'><span style='mso-special-format:nobullet; display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>First page of data: The Trait Data and Analysis Form</span><span style='font-size:106%;color:#E9EB5D; mso-color-index:3;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.34 * g_height; myleft = 0.68 * g_width; myheight = 0.09 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.68 * g_width; +yy = 0.34 * g_height; +ht = 0.09 * g_height; +wd = 0.16 * g_width; +document.write( +'<img border=0 src="slide0005_image014.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.23 * g_height; myleft = 0.84 * g_width; myheight = 0.34 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.32 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:200%;color:#E9EB5D'><i>Click </i></span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:200%;color:#E9EB5D'><i>here<br> </i></span></span></layer><script> + mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.15 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-size:200%;color:#E9EB5D'><i>to learn<br> </i></span></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-size:200%;color:#E9EB5D'><i>about<br> </i></span></div> </layer><script> + mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-size:200%;color:#E9EB5D'><i>data<br> </i></span></div> </layer><script> + mytop = 0.27 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.14 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><span style='font-size:200%;color:#E9EB5D'><i>source</i></span></div> </layer></div> </layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The Trait Data and Analysis Form is the single most important page from the point of view of working with GeneNetwork data. Please read the text carefully. Explore the links, but do not close this page. We will need it many more times in this demonstration.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. What is this database? It is called INIA Brain mRNA M430 (Apr05) PDNN, but what does that actually mean. How much of the brain was used? How were the animals processed? Most of these types of questions can be answered by clicking on the DATABASE link.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. Transcript/gene LOCATION data is usually from the most recent assembly. You can VERIFY the location of the probes and probe set using the two VERIFY buttons. VERIFY UCSC performs a sequence alignment (BLAT analysis) of the probes to the most recent assembly.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. The PROBE TOOL button provides you with highly detailed information on the probe sequences used to assemble the probe set. For example, in this case you can find out which probes correspond to which of the three exons. You can also review the performance of the individual probes. Please check the GLOSSARY for additional details on probes.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>4. The identifiers (IDs) provide links to other key resources.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0024.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0024.htm new file mode 100755 index 00000000..97f09734 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0024.htm @@ -0,0 +1,93 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0024.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = -0.01 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.97 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56'><span style='mso-special-format:nobullet; display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Data sources: Metadata for each resource</span></div> </layer></div> </layer><script> + mytop = 0.06 * g_height; myleft = 0.03 * g_width; myheight = 0.92 * g_height; mywidth = 0.6 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.03 * g_width; +yy = 0.06 * g_height; +ht = 0.92 * g_height; +wd = 0.6 * g_width; +document.write( +'<img border=0 src="slide0006_image015.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Most of the database components and resources in The GeneNetwork are linked to metadata pages that provide a human-readable summary of how, why, where, when, and with whom the data were generated. Before you get too involved with a data set, it is naturally important to read this information. While the data in The GeneNetwork may be accessible and useful, that does not always mean that the data is public domain and available for you to use in publication or for profit purposes. If you want to know more about the data ownership and usage, please read through the POLICIES pop-down menu items.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0025.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0025.htm new file mode 100755 index 00000000..32820d64 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0025.htm @@ -0,0 +1,134 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0025.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 1.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 1.07 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56'><span style='mso-special-format:nobullet; display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Expression estimates for </span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'> on the Trait Data form</span><span style='font-size:81%;color:#E9EB5D;mso-color-index:3'> </span></div> </layer></div> </layer><script> + mytop = 0.81 * g_height; myleft = 0.02 * g_width; myheight = 0.11 * g_height; mywidth = 1.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.09 * g_height; mywidth = 1.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 1.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:183%; color:#E9EB5D;mso-color-index:3'>Trait data for each strain with SE when known. For array data the scale is </span></span></layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.92 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:183%; color:#E9EB5D;mso-color-index:3'>~ log base 2.<span style="mso-spacerun: yes"> </span></span><span style='font-size:167%;color:#E9EB5D; mso-color-index:3'>F1 data = 16.723 = 2^16.723 = 108,174</span></span></layer></div> </layer></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.02 * g_width; myheight = 0.72 * g_height; mywidth = 0.51 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.02 * g_width; +yy = 0.07 * g_height; +ht = 0.72 * g_height; +wd = 0.51 * g_width; +document.write( +'<img border=0 src="slide0007_image016.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.33 * g_height; myleft = 0.57 * g_width; myheight = 0.13 * g_height; mywidth = 0.3 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.57 * g_width; +yy = 0.33 * g_height; +ht = 0.13 * g_height; +wd = 0.3 * g_width; +document.write( +'<img border=0 src="slide0007_image017.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.47 * g_height; myleft = 0.57 * g_width; myheight = 0.18 * g_height; mywidth = 0.36 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.18 * g_height; mywidth = 0.35 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.33 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D;mso-color-index: 3'>These values can all </span></span></layer><script> + mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.33 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D;mso-color-index: 3'>be changed by the </span></span></layer><script> + mytop = 0.09 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.35 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D;mso-color-index: 3'>user. (Yes, there is a </span></span></layer><script> + mytop = 0.13 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.33 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D;mso-color-index: 3'>RESET)</span></span></layer></div> </layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>This slide shows you the lower parts of the Trait Data and Analysis Form with the data for the first set of BXD strains</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0026.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0026.htm new file mode 100755 index 00000000..7dac49e1 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0026.htm @@ -0,0 +1,130 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0026.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.95 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56'><span style='mso-special-format:nobullet; display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Critiquing the </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> data the Trait Data</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.74 * g_height; myleft = 0.02 * g_width; myheight = 0.13 * g_height; mywidth = 1.1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.12 * g_height; mywidth = 1.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 1.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:150%; color:#E9EB5D;mso-color-index:3'>Use the BASIC STATISTICS button to evaluate the App data. You will find that App data </span></span></layer><script> + mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 1.09 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:150%; color:#E9EB5D;mso-color-index:3'>from the different strains are not equally trustworthy. BXD8 is an obvious outlier without </span></span></layer><script> + mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 1.03 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:150%; color:#E9EB5D;mso-color-index:3'>replication (no error bar)</span><span style='font-size:150%;color:#E9EB5D;mso-color-index:3'>. BXD33 is also suspiciously low. BXD5 is noisy. </span><span style='font-family:"Gill Sans"; font-size:150%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></span></layer></div> </layer></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.02 * g_width; myheight = 0.18 * g_height; mywidth = 0.16 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.02 * g_width; +yy = 0.07 * g_height; +ht = 0.18 * g_height; +wd = 0.16 * g_width; +document.write( +'<img border=0 src="slide0008_image018.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0.18 * g_width; myheight = 0.66 * g_height; mywidth = 0.73 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.18 * g_width; +yy = 0.08 * g_height; +ht = 0.66 * g_height; +wd = 0.73 * g_width; +document.write( +'<img border=0 src="slide0008_image019.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.87 * g_height; myleft = 0.59 * g_width; myheight = 0.13 * g_height; mywidth = 0.3 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.59 * g_width; +yy = 0.87 * g_height; +ht = 0.13 * g_height; +wd = 0.3 * g_width; +document.write( +'<img border=0 src="slide0008_image021.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The Basic Statistics page allows you to evaluate some aspects of the data quality. In this case, BXD8 is a potential problem. An outlier of this type may be generated by a technical artifact (bad sample?). However, it is also possible that BXD8 just has genuine low endogenous expression of App and may therefore be a particularly valuable model for research. There are different ways to treat problematic data of these types. One way is simply to discard this datum. The other way is to prevent outliers from have too much influence quantitatively, while leaving them in their low (or high positions). This is called windsorizing the data (after King Henry the VIII who had a habit of chopping heads). In this case, we have windsorized the BXD8 to a value of 16.0 and the BXD33 to a value of 16.02. Rank is retained. We are making a bet that the two lowest strains are really low, but we are hedging our bet and just making them a little lower than BXD90. This removes their ÒundueÓ influence.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. It turns out that BXD8 is a strain with many odd phenotypes. The whole strain is essentially an outlier for many traits. Therefore, the low App expression data may be quite accurate. Still, it would be comforting to have at least two more replicates.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0027.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0027.htm new file mode 100755 index 00000000..0a23d59d --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0027.htm @@ -0,0 +1,93 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0027.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.14 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.9 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56'><span style='mso-special-format:nobullet; display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> expression after windsorizing</span></div> </layer></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0.02 * g_width; myheight = 0.83 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.02 * g_width; +yy = 0.08 * g_height; +ht = 0.83 * g_height; +wd = 0.94 * g_width; +document.write( +'<img border=0 src="slide0009_image022.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Now we get a much better feel for the variation in the error among the cases. Those without error bars are of course the ÒnoisiestÓ of all. This data set is not complete yet (the aim is to acquire at least one male-female sample for each BXD strain).</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0028.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0028.htm new file mode 100755 index 00000000..cde4a136 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0028.htm @@ -0,0 +1,104 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0028.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.14 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56'><span style='mso-special-format:nobullet; display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Discovering shared expression patterns</span></div> </layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.03 * g_width; myheight = 0.37 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.03 * g_width; +yy = 0.1 * g_height; +ht = 0.37 * g_height; +wd = 0.94 * g_width; +document.write( +'<img border=0 src="slide0010_image023.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.38 * g_height; myleft = 0.61 * g_width; myheight = 0.14 * g_height; mywidth = 0.13 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.61 * g_width; +yy = 0.38 * g_height; +ht = 0.14 * g_height; +wd = 0.13 * g_width; +document.write( +'<img border=0 src="slide0010_image024.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Finally, we can now start an analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>We ask a simple question:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Do differences in this particular App transcript steady-state abundance level correlate with those of any other transcripts in the same INIA Brain mRNA M430 data set?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Helvetica size=3>You can CHOOSE many other DATABASES at this point if you want, but for now letÕs stick with the default.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. There are different ways to sort the correlations. The most obvious is by p-value (most significant values at the top of the list), but it is also interesting to sort the top 100 or top 500 by their gene symbol (gene ID) or by their chromosomal location (position).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. If you donÕt want your analysis to be sensitive to outliers, then you may want to choose to use the Spearman Rank Order method of calculating correlations.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0029.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0029.htm new file mode 100755 index 00000000..c296b9e9 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0029.htm @@ -0,0 +1,93 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0029.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.14 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.9 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56'><span style='mso-special-format:nobullet; display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Transcript neighborhoods</span></div> </layer></div> </layer><script> + mytop = 0.07 * g_height; myleft = 0.02 * g_width; myheight = 0.91 * g_height; mywidth = 0.85 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.02 * g_width; +yy = 0.07 * g_height; +ht = 0.91 * g_height; +wd = 0.85 * g_width; +document.write( +'<img border=0 src="slide0011_image025.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The Traits Correlation output window (Correlation Results) compares App expression data with all other traits in this INIA Brain data set. The most significant 100 or 500 transcripts are sorted by their p-values. The top correlation is that of the probe set to itself (often a value of 1.0, but in this case we modified the App values manually by windsorizing the data). The next best correlation is to another App probe set. The fourth correlation is interesting and suggests that there may be a link between App and a particular type of ataxia (Atcay).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Helvetica size=3>Use the checkboxes to the far left to select traits that you want to study together. Once you have selected interesting traits, click on the ADD SELECTION button. This puts all of the selected traits into a SELECTIONS WINDOW for other types of analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. The p-value is not corrected for multiple tests. A conservative approach for array data would be to assume 10,000 nominally independent tests. Subtract 4 from the exponent and if the value is still smaller than 0.05 you may have a real correlation.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. The LITERATURE CORRELATION is a data type generated by Drs. Ramin Homayouni and Michael Berry. Click on the header column by the asterisk for more information on this highly useful data type.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>4. We are using Pearson product moment correlations rather that the Spearman rank order correlation. But you can select either in the previous step.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0030.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0030.htm new file mode 100755 index 00000000..b84e4aad --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0030.htm @@ -0,0 +1,93 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0030.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.14 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.9 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56'><span style='mso-special-format:nobullet; display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> and </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>Atcay</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> transcript scatterplot </span></div> </layer></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0.05 * g_width; myheight = 0.91 * g_height; mywidth = 0.66 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.05 * g_width; +yy = 0.08 * g_height; +ht = 0.91 * g_height; +wd = 0.66 * g_width; +document.write( +'<img border=0 src="slide0012_image026.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>By clicking on the CORRELATION of the Atcay transcript to the App transcript, you can generate a Correlation plot between these two transcripts. In this App and Atcay scatterplot, each point is a strain mean value. For example, BXD33 and BXD8 have low App and Atcay expressions. The two parental strains and the F1 are also included in this plot.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0031.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0031.htm new file mode 100755 index 00000000..9a54b689 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0031.htm @@ -0,0 +1,93 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0031.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.14 * g_height; mywidth = 0.99 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:56'><span style='mso-special-format:nobullet; display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> transcript and eight of its neighbors</span></div> </layer></div> </layer><script> + mytop = 0.09 * g_height; myleft = 0.02 * g_width; myheight = 0.9 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.02 * g_width; +yy = 0.09 * g_height; +ht = 0.9 * g_height; +wd = 0.83 * g_width; +document.write( +'<img border=0 src="slide0013_image027.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>A group of traits from many different databases can be selected and brought together for joint analysis. In this case all of the content of the BXD SELECTIONS is from a single BRAIN database, the top 20 neighbors of the App transcript from the Correlation Results table. Eight of these neighbors plus App is shown in the slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Helvetica size=3>All of items in the BXD SELECTIONS were selected using the SELECT ALL button</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. The buttons at the top (and bottom) of this page can do some cool stuff. We will work with NETWORK GRAPH first.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. Think of the SELECTIONS as your shopping cart. You go to different aisles in the supermarket to acquire different types of items of interest. These could include transcripts, classical phenotypes (longevity, brain weight, prepulse inhibition, iron levels in midbrain). ÒChecking outÓ in this case involves doing some analysis with the items in the cart.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>4. Different tools handle different numbers of items. Most will handle up to 100 traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0032.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0032.htm new file mode 100755 index 00000000..85ee47fe --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0032.htm @@ -0,0 +1,118 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: App transcript coexpression neighborhood"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0032.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.82 * g_height; myleft = 0.04 * g_width; myheight = 0.18 * g_height; mywidth = 0.96 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div></div> </layer><script> + mytop = -0.02 * g_height; myleft = 0 * g_width; myheight = 0.12 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.02 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.04 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%'><span style='font-size:82%'><i>App</i></span><span style='font-size:82%'> transcript coexpression neighborhood</span><span style='mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.37 * g_height; myleft = 0.01 * g_width; myheight = 0.62 * g_height; mywidth = 0.97 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.37 * g_height; +ht = 0.62 * g_height; +wd = 0.97 * g_width; +document.write( +'<img border=0 src="slide0014_image029.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.11 * g_height; myleft = 0.01 * g_width; myheight = 0.25 * g_height; mywidth = 0.79 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.01 * g_width; +yy = 0.11 * g_height; +ht = 0.25 * g_height; +wd = 0.79 * g_width; +document.write( +'<img border=0 src="slide0014_image031.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.81 * g_width; myheight = 0.09 * g_height; mywidth = 0.18 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.81 * g_width; +yy = 0.1 * g_height; +ht = 0.09 * g_height; +wd = 0.18 * g_width; +document.write( +'<img border=0 src="slide0014_image033.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Output of the Network Graph. Warm colors (orange and red) are positive correlations above 0.5 whereas cool colors (green and blue) are negative correlations. Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Helvetica size=3> All of the nodes (gene/transcripts) on this graph are clickable.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. For this graph the App expression values have ÒrevertedÓ to their pre-Windsorized values.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. To generate this graph, we used the default setting:<span style="mso-spacerun: yes"> </span>Size of 16 by 16 inches; Gene Symbols; Don't Show Correlations; Use curved lines (aka ÒedgesÓ).</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0033.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0033.htm new file mode 100755 index 00000000..042ca4ad --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0033.htm @@ -0,0 +1,104 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0033.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.14 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0'><span style='mso-special-format:nobullet;display: none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Correlations of </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> with classical traits</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.28 * g_height; myleft = 0.04 * g_width; myheight = 0.7 * g_height; mywidth = 0.78 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.04 * g_width; +yy = 0.28 * g_height; +ht = 0.7 * g_height; +wd = 0.78 * g_width; +document.write( +'<img border=0 src="slide0015_image034.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0.04 * g_width; myheight = 0.19 * g_height; mywidth = 0.33 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.04 * g_width; +yy = 0.08 * g_height; +ht = 0.19 * g_height; +wd = 0.33 * g_width; +document.write( +'<img border=0 src="slide0015_image035.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Going back to the Trait Data and Analysis Form window, we have computed the correlations between strain variation in App expression level and other classical phenotypes that have already been measured in many of the same BXD strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Helvetica size=3>The number of common strains varies widely--in this case from 14 to 23 strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. We can add these traits (four are selected) to our BXD SELECTIONS window.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0034.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0034.htm new file mode 100755 index 00000000..3cf1ac70 --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0034.htm @@ -0,0 +1,93 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0034.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 0.99 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0'><span style='mso-special-format:nobullet;display: none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Network Graph of </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> with classical traits</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.08 * g_height; myleft = 0.03 * g_width; myheight = 0.9 * g_height; mywidth = 0.88 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +xx = 0.03 * g_width; +yy = 0.08 * g_height; +ht = 0.9 * g_height; +wd = 0.88 * g_width; +document.write( +'<img border=0 src="slide0016_image036.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>We have computed the Network Graph, now using other types of traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Saline Hot Plate Latency is the green node labeled 10020.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Freezing (fear) is the green node labeled 10447.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0035.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0035.htm new file mode 100755 index 00000000..ca5ac8bb --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0035.htm @@ -0,0 +1,151 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0035.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.01 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 0.93 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0'><span style='mso-special-format:nobullet;display: none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Summary of Part 1:</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0.08 * g_width; myheight = 0.47 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.9 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.88 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.84%;font-family:Arial'>1.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You have learned the basics about searching for traits<br> </span></span></layer></div> </layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.85 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-3.03%;font-family:Arial'>2.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know some methods to check data quality<br> </span></span></layer></div> </layer><script> + mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.85 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-3.03%;font-family:Arial'>3.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to edit bad or suspicious data<br> </span></span></layer></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.9 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.88 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.85%;font-family:Arial'>4.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to review the basic statistics of a trait<br> </span></span></layer></div> </layer><script> + mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.74%;font-family:Arial'>5.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to generate a scattergram between two </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>traits using the Traits Correlation tool<br> </span></span></layer></div> </layer><script> + mytop = 0.31 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.56%;font-family:Arial'>6.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to add items to your SELECTIONS window<br> </span></span></layer></div> </layer><script> + mytop = 0.37 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> + mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.97 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.57%;font-family:Arial'>7.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to generate a Network Graph of traits that </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>co-vary. </span></span></layer></div> </layer></div> </layer><script> + mytop = 0.67 * g_height; myleft = 0.05 * g_width; myheight = 0.26 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.05 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>What does genetic covariance mean? The genetic covariance can </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>be functional and mechanistic, but it can also be due to linkage </span></span></layer><script> + mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.01 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>disequilibrium. Finally, it can be due to sampling error or poor </span></span></layer><script> + mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.92 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>experimental design. Evaluate the biological plausibility of </span></span></layer><script> + mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.89 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>correlations. Test and be skeptical.</span></span></layer></div> </layer></div> </LAYER> +<script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0036.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0036.htm new file mode 100755 index 00000000..ccec2e7d --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0036.htm @@ -0,0 +1,112 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! top.PPTPRESENTATION ) { + window.location.replace( "endshow.htm" ); +} +</script> <meta name=Description content="Aug-15-05: Contact for comments and improvements:"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script> +<script language=JavaScript> +function font_size() { + var min = window.innerWidth/20; + if ( min > window.innerHeight/20 ) + min = window.innerHeight/20; + + return min+"pt"; +} +var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"]; +function restore() { + self.location.reload(); +} +function set_size() { + document.SlideLayer.width = window.innerWidth; + document.SlideLayer.height = window.innerHeight; +} +document.captureEvents(Event.MOUSEDOWN); +document.captureEvents(Event.KEYPRESS); +document.onkeypress = _KPH ; +document.onmousedown = _KPH ; + parent.base.highlite(); +</script><script language=JavaScript><!-- +function DoOnLoad() { + LoadNavSld("slide0036.htm"); +}//--> +</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> + +g_origHeight = 566; +g_origWidth = 755; +g_width = window.innerWidth - 10; +g_height = window.innerHeight - 10; + +g_top = 0; +g_left = 0; + +if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) + g_height = g_width * g_origHeight / g_origWidth; +else + g_width = g_origWidth * g_height / g_origHeight; + +g_top = (window.innerHeight - g_height) / 2; +g_left = (window.innerWidth - g_width) / 2; + +document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); +document.SlideLayer.clip.top = 0; +document.SlideLayer.clip.left = 0; +document.SlideLayer.clip.height = g_height; +document.SlideLayer.clip.width = g_width; +function new_font_size() { + var size = 11 * g_width / g_origWidth; + if ( size < 1 ) size = 1; + return size+"pt"; +} +</script> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script language=JavaScript><!-- +ht = g_height; +wd = g_width; +document.write( +'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); +//--> +</script></div> </layer><script> + mytop = 0.02 * g_height; myleft = 0.02 * g_width; myheight = 0.09 * g_height; mywidth = 0.94 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 0.92 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><span style='font-size:73%'><i>Contact for comments and improvements:</i></span><span style='font-size:82%;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> + mytop = 0.16 * g_height; myleft = 0.06 * g_width; myheight = 0.24 * g_height; mywidth = 0.9 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div><script> + mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.24 * g_height; mywidth = 0.87 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.87 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:82%'>rwilliam@nb.utmem.edu<br> </span></span></layer><script> + mytop = 0.08 * g_height; myleft = 0.04 * g_width; myheight = 0.07 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:82%'><br> </span></span></layer><script> + mytop = 0.16 * g_height; myleft = 0.04 * g_width; myheight = 0.07 * g_height; mywidth = 0.83 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-size:82%;mso-special-format:lastCR; display:none'><br> </span></span></layer></div> </layer></div> </layer><script> + mytop = 0.27 * g_height; myleft = 0.09 * g_width; myheight = 0.07 * g_height; mywidth = 0.5 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:300%; color:#E9EB5D'>kmanly@utmem.edu</span></div> </layer><script> + mytop = 0.83 * g_height; myleft = 0.04 * g_width; myheight = 0.15 * g_height; mywidth = 1.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> + mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.98 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'>The </span><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'><i>App</i></span><span style='font-family:"Gill Sans"; font-size:200%;color:#E9EB5D'> findings reviewed in this presentation are part of an </span></span></layer><script> + mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.08 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'>ongoing study by R. Williams. R. Homayouni, and R. Clark (July 15, </span></span></layer><script> + mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.91 * g_width; + document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); +</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'>2005)</span><span style='font-family:"Gill Sans";font-size:300%; color:#E9EB5D;mso-special-format:lastCR;display:none'><br> </span></span></layer></div> </layer></div> </LAYER> + <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>END</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- +//--> +</script><script language=JavaScript><!-- +function playList() { + +} +//--> +</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0037.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0037.htm new file mode 100755 index 00000000..36ca5f6f --- /dev/null +++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0037.htm @@ -0,0 +1,34 @@ +<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> +if ( ! 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This 18-slide PowerPoint side show uses the beta amyloid precursor as an example. + + <blockquote> + <UL> + <LI>View in <A Href="/tutorial/ppt/html/webqtl_demo2_part1.ppt.htm" class="normalsize">HTML</a> + <LI>Download <A Href="/tutorial/ppt/ppt/webqtl_demo2_part1.ppt" class="normalsize">Powerpoint</a> file + </UL> + </blockquote> + <P class="subtitle">WebQTL Demonstration Part II </P> + +<P>Part II: <B>A continutation that explains <B>how to map chromosomal locations (QTLs) that modulate variation in quantitative traits using the WebQTL mapping module of the GeneNetwork.</B> + + + + <blockquote> + <UL> + <LI>View in <A Href="/tutorial/ppt/html/webqtl_demo2.ppt.htm" class="normalsize">HTML</a> + <LI>Download <A Href="/tutorial/ppt/ppt/webqtl_demo2.ppt" class="normalsize">Powerpoint</a> file + </UL> + + </blockquote> + + +<P> +<P>Files last updated by RWW, July 23, 2005. + + + + + </blockquote> + </TD> + </TR></TABLE> + </TD> + </TR> + <TR> + <TD align=center bgColor=#ddddff class="solidBorder"> + <TABLE width="90%"> + <script language='JavaScript' src='/javascript/footer.js'></script> + </TABLE> + </TD> + </TR> +</TABLE> +<!-- /Footer --> +<!-- menu script itself. you should not modify this file --> +<script language="JavaScript" src="/javascript/menu_new.js"></script> +<!-- items structure. menu hierarchy and links are stored there --> +<script language="JavaScript" src="/javascript/menu_items.js"></script> +<!-- files with geometry and styles structures --> +<script language="JavaScript" src="/javascript/menu_tpl.js"></script> +<script language="JavaScript"> + <!--// + // Note where menu initialization block is located in HTML document. + // Don't try to position menu locating menu initialization block in + // some table cell or other HTML element. 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