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-<!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'>&nbsp;&nbsp;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 &quot;NR2B&quot; 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.&nbsp; </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>&nbsp;

-

-<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>&nbsp; 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&nbsp; 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 &quot;functionally&quot; spurious and can arise from linkage disequilibrium, sampling error, or (we hope rarely) poor experimental design.&nbsp; 

-

-<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>

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<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">
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<script>
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<meta name=Robots content=NoIndex>
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</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 >&gt;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p2" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('2')" id=AREF>&quot;or
  webqtl.org/search.html...&quot;</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 >&gt;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p4" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('4')" id=AREF>&quot;First page of data:&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p5" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('5')" id=AREF>&quot;Data sources:&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p6" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('6')" id=AREF>&quot;Return to Trait Data
  page&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p7" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('7')" id=AREF>&quot;Discovering shared
  expression patterns&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p8" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('8')" id=AREF>&quot;The App transcript
  neighborhood&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p9" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('9')" id=AREF>&quot;Handdrawn sketch of
  the neighborhood&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p10" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('10')" id=AREF>&quot;What a network is
  likely...&quot;</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 >&gt;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p12" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('12')" id=AREF>&quot;2.45 billion scatter
  plots&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p13" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('13')" id=AREF>&quot;Cross-tissue type
  correlations&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p14" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('14')" id=AREF>&quot;Cross-modal
  correlations:&quot;</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 >&gt;</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">&nbsp;&nbsp;&nbsp; </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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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">&nbsp;&nbsp;&nbsp; </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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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
deleted file mode 100755
index c8c72b13..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/outline_expand.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/outline_expanded.htm b/web/tutorial/ppt/WebQTLDemo_files/outline_expanded.htm
deleted file mode 100755
index 3e6bdf31..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/outline_expanded.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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 >&gt;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p2" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('2')" id=AREF>&quot;or
  webqtl.org/search.html...&quot;</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 >&gt;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p4" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('4')" id=AREF>&quot;First page of data:&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p5" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('5')" id=AREF>&quot;Data sources:&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p6" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('6')" id=AREF>&quot;Return to Trait Data
  page&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p7" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('7')" id=AREF>&quot;Discovering shared
  expression patterns&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p8" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('8')" id=AREF>&quot;The App transcript
  neighborhood&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p9" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('9')" id=AREF>&quot;Handdrawn sketch of
  the neighborhood&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p10" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('10')" id=AREF>&quot;What a network is
  likely...&quot;</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 >&gt;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p12" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('12')" id=AREF>&quot;2.45 billion scatter
  plots&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p13" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('13')" id=AREF>&quot;Cross-tissue type
  correlations&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p14" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('14')" id=AREF>&quot;Cross-modal
  correlations:&quot;</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 >&gt;</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">&nbsp;&nbsp;&nbsp; </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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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">&nbsp;&nbsp;&nbsp; </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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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>
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/outline_navigation_bar.htm b/web/tutorial/ppt/WebQTLDemo_files/outline_navigation_bar.htm
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<head>
<meta name=ProgId content=PowerPoint.Slide>
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-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=32, 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),

-   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( " > &nbsp " + 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;	
-	
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0001.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0001.htm
deleted file mode 100755
index 4c783452..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0001.htm
+++ /dev/null
@@ -1,25 +0,0 @@
-<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" );
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-</script>
<meta name=Description
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<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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</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 &#1;";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 &#1;";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">&nbsp;&nbsp; </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
deleted file mode 100755
index 5bcd338f..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0001_image001.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0001_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0001_notes_pane.htm
deleted file mode 100755
index 0df634c1..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0001_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp;&nbsp; </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
deleted file mode 100755
index 2efd97f9..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0002.htm
+++ /dev/null
@@ -1,25 +0,0 @@
-<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;
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-var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1;
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-LoadSld( gId );
-playList();MakeSldVis(1);
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-</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">&nbsp; </span>To get to a
  version of the window shown above you will need to click on the phrase<span
  style="mso-spacerun: yes">&nbsp; </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">&nbsp;
  </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
deleted file mode 100755
index 304daa18..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0002_image002.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0002_image003.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0002_image003.gif
deleted file mode 100755
index 74f73adc..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0002_image003.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0002_image004.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0002_image004.gif
deleted file mode 100755
index 1da7043d..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0002_image004.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0002_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0002_notes_pane.htm
deleted file mode 100755
index 266bf3fb..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0002_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp; </span>To get to a
  version of the window shown above you will need to click on the phrase<span
  style="mso-spacerun: yes">&nbsp; </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">&nbsp;
  </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
deleted file mode 100755
index 7e0f4be9..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0003.htm
+++ /dev/null
@@ -1,25 +0,0 @@
-<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>
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	{left:0px !important;
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<script language=JavaScript src=script.js></script><script language=JavaScript><!--

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</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
deleted file mode 100755
index 5c7d29e8..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0003_image005.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0003_image006.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0003_image006.gif
deleted file mode 100755
index f75379b9..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0003_image006.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0003_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0003_notes_pane.htm
deleted file mode 100755
index 5dbbbd2e..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0003_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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
deleted file mode 100755
index 9980cf8b..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0004.htm
+++ /dev/null
@@ -1,25 +0,0 @@
-<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" );
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<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;
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<script language=JavaScript src=script.js></script><script language=JavaScript><!--

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-playList();MakeSldVis(1);
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</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
deleted file mode 100755
index db14d732..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0004_image007.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0004_image008.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0004_image008.gif
deleted file mode 100755
index 8ac35a66..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0004_image008.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0004_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0004_notes_pane.htm
deleted file mode 100755
index 22def119..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0004_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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
deleted file mode 100755
index ab904a72..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0005.htm
+++ /dev/null
@@ -1,25 +0,0 @@
-<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 ) {
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<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;}
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</style>
<script language=JavaScript src=script.js></script><script language=JavaScript><!--

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-LoadSld( gId );
-playList();MakeSldVis(1);
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</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">&nbsp; </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><!--

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-
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-</script>
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0005_image009.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0005_image009.gif
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0005_image009.gif
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0005_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0005_notes_pane.htm
deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0005_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp; </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>
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+++ /dev/null
@@ -1,25 +0,0 @@
-<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>
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-	window.location.replace( "endshow.htm" );
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<meta name=Description content=Jun-19-03>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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</style>
<script language=JavaScript src=script.js></script><script language=JavaScript><!--

-gId="slide0006.htm"
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</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">&nbsp;&nbsp;
</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">&nbsp; </span>slide shows you the<span
  style="mso-spacerun: yes">&nbsp; </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>
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0006_image010.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0006_image010.gif
deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0006_image010.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0006_image011.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0006_image011.gif
deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0006_image011.gif
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0006_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0006_notes_pane.htm
deleted file mode 100755
index be43575c..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0006_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp; </span>slide shows you the<span
  style="mso-spacerun: yes">&nbsp; </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>
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0007.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0007.htm
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0007.htm
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@@ -1,25 +0,0 @@
-<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"
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-LoadSld( gId );
-playList();MakeSldVis(1);
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-</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>
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0007_image012.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0007_image013.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0007_image013.gif
deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0007_image013.gif
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0007_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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>
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+++ /dev/null
@@ -1,25 +0,0 @@
-<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 ) ) {
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-var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1;
-//-->

-</script><script for=window event=onload language=JavaScript><!--

-if( !IsSldOrNts() ) return;
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-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>&gt;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">&nbsp;
  </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() {
-
-}
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-</script>
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\ No newline at end of file
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+++ /dev/null
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deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0008_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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 ) {
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<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">&nbsp;
  </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>
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@@ -1,25 +0,0 @@
-<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" );
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<meta name=Description content=Jun-19-03>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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<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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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
deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0009_image015.gif
+++ /dev/null
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deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0009_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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
deleted file mode 100755
index 07768218..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0010.htm
+++ /dev/null
@@ -1,25 +0,0 @@
-<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>
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	{left:0px !important;
	width:6.0in !important;
	height:4.5in !important;
	font-size:76% !important;}
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</style>
<script language=JavaScript src=script.js></script><script language=JavaScript><!--

-gId="slide0010.htm"
-if ( !parent.base.g_done && (parent.base.msie < 0 ) ) {
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-</script><script for=window event=onload language=JavaScript><!--

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-playList();MakeSldVis(1);
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</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">&nbsp; </span>(www.lumeta.com). It actually
  illustrates the structure of connections across the<span style="mso-spacerun:
  yes">&nbsp; </span>Internet. The large green area is a major Internet
  provider (WorldCom before the fall?).<span style="mso-spacerun: yes">&nbsp;
  </span>Check<span style="mso-spacerun: yes">&nbsp; </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
deleted file mode 100755
index 6bec6eee..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0010_image016.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0010_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0010_notes_pane.htm
deleted file mode 100755
index 2b497618..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0010_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp; </span>(www.lumeta.com). It actually
  illustrates the structure of connections across the<span style="mso-spacerun:
  yes">&nbsp; </span>Internet. The large green area is a major Internet
  provider (WorldCom before the fall?).<span style="mso-spacerun: yes">&nbsp;
  </span>Check<span style="mso-spacerun: yes">&nbsp; </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>
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<head>
<meta http-equiv=Content-Type content="text/html; charset=macintosh">
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<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>
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<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 &#1;";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">&nbsp; </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>
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0011_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp; </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
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deleted file mode 100755
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@@ -1,25 +0,0 @@
-<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;
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</style>
<script language=JavaScript src=script.js></script><script language=JavaScript><!--

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<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">&nbsp; </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">&nbsp; </span>correlations come for a common reference population,
  none<span style="mso-spacerun: yes">&nbsp; </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>
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0012_image017.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0012_image017.gif
deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0012_image017.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0012_image018.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0012_image018.gif
deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0012_image018.gif
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0012_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp; </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">&nbsp; </span>correlations come for a common reference population,
  none<span style="mso-spacerun: yes">&nbsp; </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
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@@ -1,25 +0,0 @@
-<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;}
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</style>
<script language=JavaScript src=script.js></script><script language=JavaScript><!--

-gId="slide0013.htm"
-if ( !parent.base.g_done && (parent.base.msie < 0 ) ) {
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-playList();MakeSldVis(1);
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</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>
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-<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>
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<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>
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	{left:0px !important;
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<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>
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0014_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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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-</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>
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<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;
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<script language=JavaScript src=script.js></script><script language=JavaScript><!--

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-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 &#1;";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">&nbsp;&nbsp;&nbsp; </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 &#1;";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>
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0015_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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>
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<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>
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<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 ) {
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<meta name=Description content=Jun-19-03>
<link rel=Stylesheet href="master05_stylesheet.css">
<style media=print>
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</style>
<script language=JavaScript src=script.js></script><script language=JavaScript><!--

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<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%);
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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%;
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<div style='mso-line-spacing:"&#1; 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
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<div style='mso-line-spacing:"&#1; 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
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style='font-family:Times;font-size:117%;color:white;mso-special-format:lastCR;
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</span></div>

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<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:"&#1; 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:"&#1; 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:"&#1;%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:"&#1;%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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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">&nbsp;
  </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">&nbsp; </span>out during inbreeding. For example,
  there is no extant BXD3 or BXD4 strain.</font><br>
  </td>
 </tr>
</table>

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  <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">&nbsp;
  </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
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<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
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<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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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'>&gt;&gt;&gt;&gt;PROMOTER--ATG-Exon1-Intron1-Exon2-Intron2
- etc-3'UTR &gt;&gt;&gt;&gt;&gt;</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>&#4;<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>&#4;<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>&#4;<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>&#4;<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">&nbsp; </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">&nbsp;&nbsp; </span>a.<span style="mso-spacerun:
  yes">&nbsp; </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">&nbsp;&nbsp; </span>b.<span style="mso-spacerun:
  yes">&nbsp; </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">&nbsp;&nbsp; </span>c.<span style="mso-spacerun:
  yes">&nbsp; </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
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0017_image076.gif
+++ /dev/null
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deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0017_image077.gif
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deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0017_image078.gif
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+++ /dev/null
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deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0017_image080.gif
+++ /dev/null
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deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0017_image081.gif
+++ /dev/null
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deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0017_image082.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0017_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0017_notes_pane.htm
deleted file mode 100755
index a11a8b2a..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0017_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp; </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">&nbsp;&nbsp; </span>a.<span style="mso-spacerun:
  yes">&nbsp; </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">&nbsp;&nbsp; </span>b.<span style="mso-spacerun:
  yes">&nbsp; </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">&nbsp;&nbsp; </span>c.<span style="mso-spacerun:
  yes">&nbsp; </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
deleted file mode 100755
index 552d31b1..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0018.htm
+++ /dev/null
@@ -1,25 +0,0 @@
-<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" );
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<meta name=Description content="Jun-19-03: WebQTL to exploring upstream control">
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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<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 &#1;";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">&nbsp;
  </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">&nbsp; </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
deleted file mode 100755
index eb07999f..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0018_image083.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0018_image084.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0018_image084.gif
deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0018_image084.gif
+++ /dev/null
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deleted file mode 100755
index 50a3e6c2..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0018_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp;
  </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">&nbsp; </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>
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0019.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0019.htm
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0019.htm
+++ /dev/null
@@ -1,25 +0,0 @@
-<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" );
-}
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<meta name=Description
content="Jun-19-03: WebQTL to exploring upstream control.">
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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	{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><!--

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-playList();MakeSldVis(1);
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</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 &#1;";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">&nbsp; </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">&nbsp;
  </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">&nbsp; </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">&nbsp; </span>peaks at a value<span
  style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp;
  </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">&nbsp; </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
deleted file mode 100755
index 03a2878d..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0019_image085.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0019_image086.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0019_image086.gif
deleted file mode 100755
index 3327e4da..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0019_image086.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0019_image087.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0019_image087.gif
deleted file mode 100755
index 227fce55..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0019_image087.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0019_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0019_notes_pane.htm
deleted file mode 100755
index cbe88cf0..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0019_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp; </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">&nbsp;
  </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">&nbsp; </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">&nbsp; </span>peaks at a value<span
  style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp;
  </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">&nbsp; </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
deleted file mode 100755
index d21bef3e..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0020.htm
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@@ -1,25 +0,0 @@
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<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 ) {
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<meta name=Description content="Jun-19-03: The whole neighborhood is modulated!">
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<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 &#1;";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">&nbsp;
  </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() {
-
-}
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-</script>
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\ 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
deleted file mode 100755
index 4e9f96be..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0020_image088.gif
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0020_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0020_notes_pane.htm
deleted file mode 100755
index 78ea1866..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0020_notes_pane.htm
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@@ -1,5 +0,0 @@
-<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>
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<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">&nbsp;
  </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
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<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>
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-if( MakeNotesVis() ) return;
-LoadSld( gId );
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<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 &#1;";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>&amp;<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">&nbsp;</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">&nbsp; </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>
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0021_image089.gif
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0021_image090.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0021_image090.gif
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0021_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp;</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">&nbsp; </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>
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+++ /dev/null
@@ -1,25 +0,0 @@
-<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;}
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</style>
<script language=JavaScript src=script.js></script><script language=JavaScript><!--

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-</script><script for=window event=onload language=JavaScript><!--

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-if( MakeNotesVis() ) return;
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-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">&nbsp;
  </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>
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0022_image092.gif
+++ /dev/null
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deleted file mode 100755
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deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0022_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp;
  </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>
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0023.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0023.htm
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+++ /dev/null
@@ -1,25 +0,0 @@
-<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"
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-</script><script for=window event=onload language=JavaScript><!--

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-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">&nbsp; </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">&nbsp; </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
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deleted file mode 100755
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deleted file mode 100755
index 418d3b45..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0023_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp; </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">&nbsp; </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>
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deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0024.htm
+++ /dev/null
@@ -1,25 +0,0 @@
-<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>
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	{left:0px !important;
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-LoadSld( gId );
-playList();MakeSldVis(1);
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-</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>
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0024_image101.gif
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deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0024_image102.gif
+++ /dev/null
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deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0024_image104.gif
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deleted file mode 100755
index 3a7bdfa1..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0024_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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>
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0025.htm
+++ /dev/null
@@ -1,25 +0,0 @@
-<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;
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-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 &#1;";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">&nbsp;</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>
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deleted file mode 100755
index 242e4087..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0025_image105.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0025_image106.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0025_image106.gif
deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0025_image106.gif
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deleted file mode 100755
index ef04157c..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0025_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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>
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0026.htm
+++ /dev/null
@@ -1,25 +0,0 @@
-<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;
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-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 &#1;";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">&nbsp;&nbsp;&nbsp; </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 &#1;";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">&nbsp; </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">&nbsp; </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>

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-
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0026_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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 ) {
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</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">&nbsp; </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">&nbsp; </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>

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<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>
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<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>
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<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 &#1;";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 &#1;";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">&nbsp; </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>

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-
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0027_image108.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0027_image108.gif
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0027_image108.gif
+++ /dev/null
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deleted file mode 100755
index 9614c538..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0027_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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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</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">&nbsp; </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>
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<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>
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href=WebQTLDemo.ppt>
<script>
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<meta name=Description
content="Jun-19-03: Direct correlations between genotypes and traits">
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<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
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style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>

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<div class=T style='mso-line-spacing:" 0 &#1;";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">&nbsp; </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>
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0028_image110.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0028_image110.gif
deleted file mode 100755
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0028_image111.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0028_image111.gif
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index 89b67431..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0028_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp; </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>
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+++ /dev/null
@@ -1,25 +0,0 @@
-<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" );
-}
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<meta name=Description
content="Jun-19-03: WhatÕs downstream of Chr 2 near Hars2?">
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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	width:6.0in !important;
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-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 &#1;";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 &#1;";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">&nbsp; </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>
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deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0029_image112.gif
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deleted file mode 100755
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0029_image113.gif
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0029_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp; </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>
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0030.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0030.htm
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-<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"
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-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 &#1;";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>
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0030_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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>
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@@ -1,25 +0,0 @@
-<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" );
-}
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<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;}
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</style>
<script language=JavaScript src=script.js></script><script language=JavaScript><!--

-gId="slide0031.htm"
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-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 &#1;";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">&nbsp; </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>

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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0031_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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>
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</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">&nbsp; </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>
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deleted file mode 100755
index 60a1bee2..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0032.htm
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<head>
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<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
genomics</title>
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href=WebQTLDemo.ppt>
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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 &#1;";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 &#1;";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>

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<table style='color:white' border=0 width="100%">
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  <td width="100%"></td>
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0032_notes_pane.htm
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<head>
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<body bgcolor=black text=white>

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</table>

</body>

</html>
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0033.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0033.htm
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--- a/web/tutorial/ppt/WebQTLDemo_files/slide0033.htm
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@@ -1,153 +0,0 @@
-<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>
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<div><script>
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<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%;
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One<br>
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</i></span></span></layer></div>

</layer></div>

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<div style='text-align:left;font-family:"Gill Sans";font-weight:normal;
font-style:normal;text-decoration:none;text-shadow:none;text-effect:none;
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<div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
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color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
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<div style='mso-line-spacing:" 0 &#1;";mso-margin-left-alt:348;mso-text-indent-alt:
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targets</span></span></layer></div>

</layer></div>

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<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
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</layer><script>
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<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
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</span></div>

</layer></div>

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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%;
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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>
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  </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">&nbsp;&nbsp; </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>
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0034.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0034.htm
deleted file mode 100755
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color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
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webqtl.org/search.html (mirror)</span></div>

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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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<div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
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<div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
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</i></span></div>

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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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<div>

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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>

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   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>
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  </tr>
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   <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
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   a version of the window shown above you will need to click on the phrase<span
   style="mso-spacerun: yes">&nbsp; </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">&nbsp;
   </span>a problem: try the mirror site http://webqtl.org/search.html.</font><br>
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<div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
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</i></span></div>

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<div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
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display:none'><br>
</span></div>

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<div style='text-align:left;font-family:"Gill Sans";font-weight:normal;
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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'>
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   <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><!--

-//-->

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</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
deleted file mode 100755
index ae7843aa..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0036.htm
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-<html>

<head>
<meta name=ProgId content=PowerPoint.Slide>
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<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
genomics</title>
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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>

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<div><script language=JavaScript><!--

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<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:
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<div><span style='font-size:200%;color:#E9EB5D'><i>Click here<br>
</i></span></div>

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<div><span style='font-size:200%;color:#E9EB5D'><i>to learn<br>
</i></span></div>

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<div><span style='font-size:200%;color:#E9EB5D'><i>about<br>
</i></span></div>

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<div><span style='font-size:200%;color:#E9EB5D'><i>data<br>
</i></span></div>

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<div><span style='font-size:200%;color:#E9EB5D'><i>source</i></span></div>

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 <div id=NotesObj style='display:none'>
 <table style='color:white' border=0 width="100%">
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  </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><!--

-//-->

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</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
deleted file mode 100755
index bb776db5..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0037.htm
+++ /dev/null
@@ -1,93 +0,0 @@
-<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>
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<script>
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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>

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<div><script language=JavaScript><!--

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<layer>
 <div id=NotesObj style='display:none'>
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   <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">&nbsp; </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>
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<script language=JavaScript><!--

-//-->

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\ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0038.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0038.htm
deleted file mode 100755
index b3e613ca..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0038.htm
+++ /dev/null
@@ -1,119 +0,0 @@
-<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>
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For array data </span></span></layer><script>
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0039.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0039.htm
deleted file mode 100755
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0040.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0040.htm
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  </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">&nbsp; </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>
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color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
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neighborhood</span></div>

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  </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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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>
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<div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans";
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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:
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 <div id=NotesObj style='display:none'>
 <table style='color:white' border=0 width="100%">
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   <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">&nbsp; </span>(www.lumeta.com). It actually
   illustrates the structure of connections across the<span
   style="mso-spacerun: yes">&nbsp; </span>Internet. The large green area is a
   major Internet provider (WorldCom before the fall?).<span
   style="mso-spacerun: yes">&nbsp; </span>Check<span style="mso-spacerun:
   yes">&nbsp; </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>
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@@ -1,112 +0,0 @@
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<head>
<meta name=ProgId content=PowerPoint.Slide>
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<script>
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   <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">&nbsp; </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>
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  </tr>
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color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
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is one of the best</span></div>

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   <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">&nbsp; </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">&nbsp; </span>correlations come for a common reference population,
   none<span style="mso-spacerun: yes">&nbsp; </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>
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color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
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correlations</span></div>

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   <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>
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   <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>
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</i></span></span></layer></div>

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<div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
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<div style='mso-line-spacing:" 0 &#1;";mso-margin-left-alt:348;mso-text-indent-alt:
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   <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>
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-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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;mso-line-spacing:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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>

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   <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">&nbsp; </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">&nbsp; </span>out during inbreeding. For
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</layer><script>
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-	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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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'>&gt;&gt;&gt;&gt;PROMOTER--ATG-Exon1-Intron1-Exon2-Intron2
- etc-3'UTR &gt;&gt;&gt;&gt;&gt;</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>&#4;<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>&#4;<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>&#4;<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>&#4;<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;
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<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
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</span></div>

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  </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">&nbsp; </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">&nbsp;&nbsp; </span>a.<span style="mso-spacerun:
   yes">&nbsp; </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">&nbsp;&nbsp; </span>b.<span style="mso-spacerun:
   yes">&nbsp; </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">&nbsp;&nbsp; </span>c.<span style="mso-spacerun:
   yes">&nbsp; </span>may be contingent on environmental factors (heat shock
   may trigger the expression of a polymorphic factor that affects mRNA
   abundance).</font><br>
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  </tr>
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0050.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0050.htm
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control</i></span></div>

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mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:217%;
color:#FF0F0F'>Just click</span></div>

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 <table style='color:white' border=0 width="100%">
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   <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">&nbsp;
   </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">&nbsp; </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>
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\ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0051.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0051.htm
deleted file mode 100755
index 39d20b2b..00000000
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<div><span style='font-size:267%;color:#E9EB5D'><i>Is App modulated by Chr
2?<br>
</i></span></div>

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<div><span style='font-size:267%;color:#E9EB5D'><i>Probably, but donÕt bet the
farm. </i></span></div>

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 <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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </span>peaks at a value<span
   style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp;
   </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">&nbsp; </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>

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mso-text-raise:0%;mso-line-spacing:" 0 &#1;";mso-line-spacing:" 0 &#1;"'><span
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modulated!</i></span></div>

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  <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">&nbsp;
   </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>
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<br>
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<div style='text-align:center'><span style='font-size:267%;color:#E9EB5D'><i>high
r</i></span></div>

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<div style='text-align:center'><span style='font-size:267%;color:#E9EB5D'><i>candidates</i></span></div>

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 <div id=NotesObj style='display:none'>
 <table style='color:white' border=0 width="100%">
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   <td width="100%"></td>
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  <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">&nbsp;</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">&nbsp; </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>
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\ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0054.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0054.htm
deleted file mode 100755
index 1e0d7468..00000000
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</i></span></span></layer></div>

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   <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:
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<script language=JavaScript><!--

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\ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0055.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0055.htm
deleted file mode 100755
index 36b2d736..00000000
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no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%;
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style='font-size:150%;color:black;mso-special-format:lastCR;display:none'><b><br>
</b></span></div>

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  </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">&nbsp; </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">&nbsp; </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>
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\ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0056.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0056.htm
deleted file mode 100755
index 43ebf6d5..00000000
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  <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>
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\ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0057.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0057.htm
deleted file mode 100755
index 9a7adf61..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0057.htm
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@@ -1,122 +0,0 @@
-<html>

<head>
<meta name=ProgId content=PowerPoint.Slide>
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<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
genomics</title>
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href=WebQTLDemo.ppt>
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link Hars2 with App? </i></span></div>

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NCBI, <br>
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  <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>
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0058.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0058.htm
deleted file mode 100755
index 9feed242..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0058.htm
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<head>
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<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
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</i></span></span></layer></div>

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<div style='text-align:left;font-family:"Gill Sans";font-weight:normal;
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</span></span></layer></div>

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targets</span></span></layer></div>

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<div></div>

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   <td align=left colspan=1><font face=Helvetica size=3>Part 3.<span
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  <tr>
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   <td align=left colspan=1><br>
   </td>
  </tr>
  <tr>
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   <td align=left colspan=1><font face=Helvetica size=3>In a genetic and
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   but unless it is polymorphic between C57BL/6J and DBA/2J, then it cannot
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<script language=JavaScript><!--

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\ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0059.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0059.htm
deleted file mode 100755
index a479ea68..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0059.htm
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<head>
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</span></div>

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<div><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>App
and many other<br>
</i></span></div>

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style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%;
color:#E9EB5D'><i>other traits.</i></span></span></layer></div>

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 <div id=NotesObj style='display:none'>
 <table style='color:white' border=0 width="100%">
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  </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">&nbsp; </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>
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\ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0060.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0060.htm
deleted file mode 100755
index aa804b9a..00000000
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<div style='text-align:left;font-family:"Gill Sans";font-weight:normal;
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style='font-size:82%;mso-special-format:lastCR;display:none'><br>
</span></div>

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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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<div><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>App
and<br>
</i></span></div>

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-

<layer>
 <div id=NotesObj style='display:none'>
 <table style='color:white' border=0 width="100%">
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   <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">&nbsp; </span>This is in essence a
   backwards way of mapping QTLs. We are considering one marker and asking what
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 </div>
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<script language=JavaScript><!--

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\ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0061.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0061.htm
deleted file mode 100755
index cce3b81c..00000000
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@@ -1,124 +0,0 @@
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<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
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  <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">&nbsp; </span>But we have circled one transcript,
   actinin alpha 2, that has a moderately good correlation (0.59) with
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   near D2Mit423</font><br>
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0062.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0062.htm
deleted file mode 100755
index c8c24f70..00000000
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style='font-size:82%'><i>WhatÕs downstream of Chr 2 near Hars2?</i></span><span
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</span></div>

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   <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
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0063.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0063.htm
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</span></div>

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 <div id=NotesObj style='display:none'>
 <table style='color:white' border=0 width="100%">
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  </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">&nbsp; </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>
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\ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0064.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0064.htm
deleted file mode 100755
index f75dd8f4..00000000
--- a/web/tutorial/ppt/WebQTLDemo_files/slide0064.htm
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@@ -1,100 +0,0 @@
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<head>
<meta name=ProgId content=PowerPoint.Slide>
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<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
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index 5aa0f55d..00000000
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deleted file mode 100755
index 8f728017..00000000
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deleted file mode 100755
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deleted file mode 100755
index 8cfab86e..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/fullscreen.htm
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<script>
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-
-
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/master02.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/master02.htm
deleted file mode 100755
index b696e328..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/master02.htm
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@@ -1,11 +0,0 @@
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<div class=O style='text-align:right;position:absolute;top:.53%;left:58.01%;
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/master03.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/master03.htm
deleted file mode 100755
index a31d27f9..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/master03.htm
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@@ -1,11 +0,0 @@
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deleted file mode 100755
index abdc767d..00000000
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deleted file mode 100755
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  <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID8 VISIBILITY=hidden >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p12" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('12')" id=AREF>&quot;Summary of Part 2&quot;</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 >&gt;</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 >&gt;</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
deleted file mode 100755
index 85b11c52..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_navigation_bar.htm
+++ /dev/null
@@ -1,37 +0,0 @@
-<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><script language=JavaScript><!--

-
-function restore() {
-if( navigator.platform != "MacPPC" )
-	self.location.reload();
-}
-
-function writebody() {
-
-	if ( parent.g_showoutline ) {
-			document.write('<table border=0 valign=top cellspacing=0 width=\"100%\">' + 
-			'<tr valign=top><td align=left valign=top>' );
-			  document.write( '<a href=\"javascript:parent.ToggleOutline()\" ><img src=\"outline.gif\" title=\"Show/Hide Outline\" alt=\"Show/Hide Outline\" border=0></a>' );
-			  document.write( '</td>' );
-		if( parent.g_outline_href == parent.OUTLINE_EXPAND_HREF ) {
-			document.write( '<td align=right valign=top><a href=\"javascript:parent.CollapseOutline()\">' +
-			'<img src="outline_collapse.gif" title="Collapse Outline" alt="Collapse Outline" border=0>' +  
-			'</a></td>');
-		} else {
-			document.write('<td align=right valign=top><a href=\"javascript:parent.ExpandOutline()\">' +
-			'<img src="outline_expand.gif" title="Expand Outline" alt="Expand Outline" border=0>' + 
-			 '</a></td>');
-		}
-		document.write("</tr></table>");
-	}
-	else {
-			document.write( '<table border=0 valign=top cellspacing=0 width=\"100%\"><td align=\"left\"><a href=\"javascript:parent.ToggleOutline()\" ><img border=0 src=\"outline.gif\" title=\"Show/Hide Outline\" alt=\"Show/Hide Outline\"></a></td></table>' );
-	}
-}//-->

-</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.ppt_files/prev_active.gif b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/prev_active.gif
deleted file mode 100755
index 004a872f..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/prev_active.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/prev_disabled.gif b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/prev_disabled.gif
deleted file mode 100755
index 8a467185..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/prev_disabled.gif
+++ /dev/null
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/script.js b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/script.js
deleted file mode 100755
index 8110ab9a..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/script.js
+++ /dev/null
@@ -1,1343 +0,0 @@
-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=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( " > &nbsp " + 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
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001.htm
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<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
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style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>

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mso-text-indent-alt:0;position:absolute;top:11.65%;left:.96%;width:98.2%;
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style='font-size:73%'>The GeneNetwork and WebQTL : PART 2<span
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</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:
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</i></span></span></div>

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filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>

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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&#8211;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&#8211;29)</span></span></div>

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style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E;
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<table style='color:white' border=0 width="100%">
 <tr>
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  <td width="100%"></td>
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 <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>
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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
deleted file mode 100755
index a1cb20e4..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_image001.png
+++ /dev/null
diff --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
deleted file mode 100755
index e06bd0db..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_image002.png
+++ /dev/null
diff --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
deleted file mode 100755
index 9e0445f3..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_notes_pane.htm
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  <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>
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<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">&nbsp; </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>

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-<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">
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<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">&nbsp; </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>
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<link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm">
<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
genomics</title>
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href="webqtl_demo2.ppt.ppt">
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<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'>&gt;&gt;&gt;&gt;PROMOTER--ATG-Exon1-Intron1-Exon2-Intron2
- etc-3'UTR &gt;&gt;&gt;&gt;&gt;</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>&#4;</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>&#4;</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>&#4;</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>&#4;</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">&nbsp; </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">&nbsp;&nbsp; </span>a.<span style="mso-spacerun:
  yes">&nbsp; </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">&nbsp;&nbsp; </span>b.<span style="mso-spacerun:
  yes">&nbsp; </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">&nbsp;&nbsp; </span>c.<span style="mso-spacerun:
  yes">&nbsp; </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>

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<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">&nbsp; </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">&nbsp;&nbsp; </span>a.<span style="mso-spacerun:
  yes">&nbsp; </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">&nbsp;&nbsp; </span>b.<span style="mso-spacerun:
  yes">&nbsp; </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">&nbsp;&nbsp; </span>c.<span style="mso-spacerun:
  yes">&nbsp; </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>
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<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>
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<meta name=Description content="Aug-15-05: Discovering upstream modulatory loci">
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<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">&nbsp; </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">&nbsp; </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>
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@@ -1,5 +0,0 @@
-<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">&nbsp; </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">&nbsp; </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>
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-<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" );
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-</script>
<meta name=Description
content="Aug-15-05: WebQTL searches for upstream controllers">
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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	{left:0px !important;
	width:6.0in !important;
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</style>
<script language=JavaScript src=script.js></script><script language=JavaScript><!--

-gId="slide0005.htm"
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-</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">&nbsp; </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">&nbsp;
  </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">&nbsp; </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">&nbsp; </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>
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<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">
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<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">&nbsp; </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">&nbsp;
  </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">&nbsp; </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">&nbsp; </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>

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genomics</title>
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<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
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<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>

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-<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">
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<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>
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<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
genomics</title>
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href="webqtl_demo2.ppt.ppt">
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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">&nbsp; </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>

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-<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
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<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">&nbsp; </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
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<head>
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<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
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<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">
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<meta name=Description content="Aug-15-05: Evaluating candidate genes">
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<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">&nbsp;</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">&nbsp; </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">&nbsp;&nbsp; </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">&nbsp;
  </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>

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--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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>
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</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">&nbsp; </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">&nbsp;&nbsp; </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">&nbsp;
  </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>
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<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">
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<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
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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>

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<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"
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<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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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>

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<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">
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<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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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>
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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">&nbsp; </span>Ctbp2 is a strong cis QTL in some brain regions (here the
  data are taken from the striatum).<span style="mso-spacerun: yes">&nbsp;
  </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">&nbsp; </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>

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-<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>
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<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">&nbsp; </span>Ctbp2 is a strong cis QTL in some brain regions (here the
  data are taken from the striatum).<span style="mso-spacerun: yes">&nbsp;
  </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">&nbsp; </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>

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genomics</title>
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href="webqtl_demo2.ppt.ppt">
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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">&nbsp;
  </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">&nbsp; </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>
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--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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>
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</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">&nbsp;
  </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">&nbsp; </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>
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<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
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<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">
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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">&nbsp;</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">&nbsp;</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">&nbsp;</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">&nbsp;</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">&nbsp;</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>

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-<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 ) {
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</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>
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<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>
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<meta name=Description content="Aug-15-05: Test Questions">
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<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>

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-<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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</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>

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<head>
<meta http-equiv=Content-Type content="text/html; charset=macintosh">
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<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>
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<meta name=Description
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<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%);
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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%">
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  <td width=5 nowrap></td>
  <td width="100%"></td>
 </tr>
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  <td colspan=1></td>
  <td align=left colspan=1><font face=Verdana size=3>END</font><br>
  </td>
 </tr>
</table>

</div>

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<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">
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<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
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<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;
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-</script><span
style='text-align:left'><span style='font-size:73%'>The GeneNetwork and WebQTL
: PART 2<span style="mso-spacerun: yes">&nbsp;&nbsp; </span><br>
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</i></span></span></layer></div>

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style='text-align:left'><span style='mso-special-format:nobullet;display:none;
color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
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style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index:
3'>(slides 2&#8211;17)<br>
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color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
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display:none'><br>
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</LAYER>

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<layer>
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  </tr>
  <tr>
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   <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>
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@@ -1,5 +0,0 @@
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<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
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  <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
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  <td align=left colspan=1><font face=Arial size=2>1.</font><font
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 </tr>
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  <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>
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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;
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  </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">&nbsp;
   </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>
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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
deleted file mode 100755
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--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016_image036.png
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--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
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<head>
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<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
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  <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
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  </td>
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  <td colspan=1></td>
  <td align=left colspan=1><font face=Helvetica size=2>Freezing (fear) is the
  green node labeled 10447.</font><br>
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  <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br>
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0017.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0017.htm
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<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>
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   <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>
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   <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>
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   <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">&nbsp; </span>The way
   in which an upstream polymorphism influences a downstream difference in mRNA
   abundance can be indirect. Effects can:</font><br>
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   style="mso-spacerun: yes">&nbsp;&nbsp; </span>b.<span style="mso-spacerun:
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   during development but has permanent effects in adults)</font><br>
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   <td align=left colspan=1><font face=Helvetica size=3><span
   style="mso-spacerun: yes">&nbsp;&nbsp; </span>c.<span style="mso-spacerun:
   yes">&nbsp; </span>may be contingent on environmental factors (heat shock
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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>

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   <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">&nbsp; </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">&nbsp; </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>
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<script language=JavaScript><!--

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@@ -1,5 +0,0 @@
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<head>
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<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm">
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  <td width="100%"></td>
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 <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>
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019.htm
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--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019.htm
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@@ -1,155 +0,0 @@
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<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
genomics</title>
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<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%;
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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>

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style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>locus is
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lastCR;display:none'><i><br>
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 <div id=NotesObj style='display:none'>
 <table style='color:white' border=0 width="100%">
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   <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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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><!--

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-</script><script language=JavaScript><!--

-function playList() {
-
-}
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</body>

</html>
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<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">&nbsp; </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>

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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:
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</i></span></div>

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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>
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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:
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   <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>
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  <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">&nbsp; </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">&nbsp;&nbsp; </span>a.<span style="mso-spacerun:
  yes">&nbsp; </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">&nbsp;&nbsp; </span>b.<span style="mso-spacerun:
  yes">&nbsp; </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">&nbsp;&nbsp; </span>c.<span style="mso-spacerun:
  yes">&nbsp; </span>may be contingent on environmental factors (heat shock may
  trigger the expression of a polymorphic factor that affects mRNA abundance).</font><br>
  </td>
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<div><script>
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<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>
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<div><script>
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<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>

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<div><script language=JavaScript><!--

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</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">&nbsp; </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><!--

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-//-->

-</script>
</body>

</html>
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+++ /dev/null
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+++ /dev/null
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deleted file mode 100755
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--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">
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<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">&nbsp; </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">&nbsp; </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>
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022.htm
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index 25d9a02e..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022.htm
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@@ -1,134 +0,0 @@
-<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>
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href="webqtl_demo2.ppt.ppt">
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<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>
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<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>
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<div style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>Right
position<br>
</i></span></div>

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<div style='text-align:center'><script>
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style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>and
high </i></span></span></layer><script>
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style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>correlation</i></span></span></layer></div>

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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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<div style='text-align:center'><span style='font-size:267%;color:#E9EB5D'><i><span
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color:#E9EB5D'><i>= better<br>
</i></span></div>

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<div style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>candidates</i></span></div>

</layer></div>

</layer></div>

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-

<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">&nbsp; </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">&nbsp;&nbsp; </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">&nbsp;
   </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>
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 <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">&nbsp; </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">&nbsp;
  </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">&nbsp; </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">&nbsp; </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>

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   <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">&nbsp; </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>
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  <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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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>
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  <td width="100%"></td>
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 <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>

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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>

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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>This is</span><span
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</i></span></span></layer></div>

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style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>This is</span><span
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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>

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 <div id=NotesObj style='display:none'>
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   <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">&nbsp; </span>Ctbp2 is a strong cis QTL in some
   brain regions (here the data are taken from the striatum).<span
   style="mso-spacerun: yes">&nbsp; </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>
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   <td colspan=1></td>
   <td align=left colspan=1><br>
   </td>
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   <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">&nbsp; </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>
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-<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">
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href="webqtl_demo2.ppt.ppt">
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<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>
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  <td colspan=1></td>
  <td align=left colspan=1><font face=Verdana size=2>Notes:</font><br>
  </td>
 </tr>
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  <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">&nbsp; </span>These physical maps
  are zoomable, a feature we will exploit to evaluate candidate genes in this
  QTL interval.</font><br>
  </td>
 </tr>
</table>

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font-style:normal;text-decoration:none;text-shadow:none;text-effect:none;
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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>

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<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">&nbsp;
   </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">&nbsp; </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>
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   <td colspan=1></td>
   <td align=left colspan=1><br>
   </td>
  </tr>
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   <td align=left colspan=1><br>
   </td>
  </tr>
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  <td width="100%"></td>
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 <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">&nbsp; </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">&nbsp;&nbsp; </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">&nbsp;
  </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>

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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>

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analysis and mapping.<br>
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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">&nbsp;</span>Reviewed difference between
genetic and physical maps.<br>
</span></span></layer></div>

</layer><script>
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<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;
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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">&nbsp;</span>Discussed interpreting features
of QTL maps including the LRS function, </span></span></layer><script>
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-</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>
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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>
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<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:
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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">&nbsp;</span>Illustrated techniques to
generate a list of positional candidates.<br>
</span></span></layer></div>

</layer><script>
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<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:
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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">&nbsp;</span>Discussed some factors used to
evaluate candidate genes.</span></span></layer></div>

</layer></div>

</layer><script>
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<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>
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-</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>
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-</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>
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-</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>
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-</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>
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-</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>

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-<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">
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<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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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>
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@@ -1,115 +0,0 @@
-<html>

<head>
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<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
genomics</title>
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href="webqtl_demo2.ppt.ppt">
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<meta name=Description content="Aug-15-05: Test Questions">
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<div><script>
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<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>
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<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>
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<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>
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-</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>
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-</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>

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<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>
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-	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>
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-</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>
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-</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>
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<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%;
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-</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>
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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>

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-<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">
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href="webqtl_demo2.ppt.ppt">
<script>
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<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">&nbsp; </span>Ctbp2 is a strong cis QTL in some brain regions (here the
  data are taken from the striatum).<span style="mso-spacerun: yes">&nbsp;
  </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>
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  <td colspan=1></td>
  <td align=left colspan=1><br>
  </td>
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  <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">&nbsp; </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>

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-<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
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<div><script>
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<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>
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<div><script>
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<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>
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-	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>
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style='text-align:left'><span style='font-size:82%'><br>
</span></span></layer><script>
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style='text-align:left'><span style='font-size:82%;mso-special-format:lastCR;
display:none'><br>
</span></span></layer></div>

</layer></div>

</layer><script>
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<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>
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<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>
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-	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>
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-</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>
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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>

-

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   <td align=left colspan=1><font face=Verdana size=3>END</font><br>
   </td>
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-<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>
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<body bgcolor=black text=white>

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  <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">&nbsp;
  </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">&nbsp; </span>with several transcription factors
  including EVI1, ZFPM1, and<span style="mso-spacerun: yes">&nbsp;&nbsp;
  </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>
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  <td colspan=1></td>
  <td align=left colspan=1><br>
  </td>
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  <td colspan=1></td>
  <td align=left colspan=1><font face=Verdana size=2>Notes:</font><br>
  </td>
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 <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">&nbsp;
  </span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene<span
  style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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>
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  <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>
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\ 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
deleted file mode 100755
index 4e705866..00000000
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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>

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   <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">&nbsp;
   </span>Size of 16 by 16 inches; Gene Symbols; Don't Show Correlations; Use
   curved lines (aka ÒedgesÓ).</font><br>
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\ 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
deleted file mode 100755
index 93429543..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0046.htm
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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
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 <div id=NotesObj style='display:none'>
 <table style='color:white' border=0 width="100%">
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   <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>
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   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
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   </td>
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0047.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0047.htm
deleted file mode 100755
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<div><script>
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<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>

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<div><script language=JavaScript><!--

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</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() {
-
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-//-->

-</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
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<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
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<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>
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<div>

<layer>
 <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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 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%;
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</layer>

<layer>
 <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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</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>
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-</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>
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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">&nbsp;</span>You have learned the basics
about searching for traits<br>
</span></span></layer></div>

</layer><script>
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<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>
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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">&nbsp;</span>You know some methods to check
data quality<br>
</span></span></layer></div>

</layer><script>
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<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">&nbsp;</span>You know how to edit bad or
suspicious data<br>
</span></span></layer></div>

</layer><script>
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-</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">&nbsp;</span>You know how to review the
basic statistics of a trait<br>
</span></span></layer></div>

</layer><script>
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<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>
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-	document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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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">&nbsp;</span>You know how to generate a
scattergram between two </span></span></layer><script>
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-</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>
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<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 + ' >' );
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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">&nbsp;</span>You know how to add items to
your SELECTIONS window<br>
</span></span></layer></div>

</layer><script>
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<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;
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-</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">&nbsp;</span>You know how to generate a
Network Graph of traits that </span></span></layer><script>
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-</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>
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<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>
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-</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>
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   <td align=left colspan=1><font face=Helvetica size=3>Part 2: Discovering
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</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;
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   <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>
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   <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">&nbsp;
   </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>
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   <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br>
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   <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>
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   <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>
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  </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
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   therefore contains as many recombinations as about 260 F2 animals.</font><br>
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-</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>

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   <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>
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   <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
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   in enhancers or may be in 3Õ UTR binding sites that affect message
   stability.</font><br>
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   <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">&nbsp; </span>The way
   in which an upstream polymorphism influences a downstream difference in mRNA
   abundance can be indirect. Effects can:</font><br>
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   style="mso-spacerun: yes">&nbsp;&nbsp; </span>b.<span style="mso-spacerun:
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   <td align=left colspan=1><font face=Helvetica size=3><span
   style="mso-spacerun: yes">&nbsp;&nbsp; </span>c.<span style="mso-spacerun:
   yes">&nbsp; </span>may be contingent on environmental factors (heat shock
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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
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none'><i><br>
</i></span></div>

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  </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">&nbsp; </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">&nbsp; </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>
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font-style:normal;text-decoration:none;text-shadow:none;text-effect:none;
mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%;
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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;
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</i></span></div>

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   <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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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>
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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:
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style='text-align:left'><span style='font-size:117%;color:#E9EB5D'><i>The
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between New York and Boston in either travel hours or kilometers</i></span><span
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   <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>
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  <tr>
   <td colspan=1></td>
   <td align=left colspan=1><font face=Verdana size=3>Also notice the large
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   <td align=left colspan=1><font face=Verdana size=3>The physical scale is
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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>

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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:
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</i></span></div>

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 <div id=NotesObj style='display:none'>
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  </tr>
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   <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">&nbsp; </span>These physical maps
   are zoomable, a feature we will exploit to evaluate candidate genes in this
   QTL interval.</font><br>
   </td>
  </tr>
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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>

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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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<div style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>Right
position<br>
</i></span></div>

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</i></span></div>

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<div style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>candidates</i></span></div>

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 <div id=NotesObj style='display:none'>
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  </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">&nbsp; </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">&nbsp;&nbsp; </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">&nbsp;
   </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>
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<layer>
 <div id=NotesObj style='display:none'>
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  </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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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>
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0058.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0058.htm
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<div style='text-align:left;font-family:"Gill Sans";font-weight:normal;
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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>

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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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data set. </span><span style='font-size:233%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><i><br>
</i></span></span></layer></div>

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  </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">&nbsp; </span>Ctbp2 is a strong cis QTL in some
   brain regions (here the data are taken from the striatum).<span
   style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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>
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0059.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0059.htm
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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
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</i></span></div>

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   <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">&nbsp;
   </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">&nbsp; </span>with several transcription factors
   including EVI1, ZFPM1, and<span style="mso-spacerun: yes">&nbsp;&nbsp;
   </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">&nbsp;
   </span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene<span
   style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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>
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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
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display:none'><br>
</span></div>

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<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;
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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:
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analysis and mapping.<br>
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genetic and physical maps.<br>
</span></span></layer></div>

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color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
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style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
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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>

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</span></span></layer></div>

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text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;
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<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>
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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
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%;
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variation in the </span></span></layer><script>
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%;
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%;
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skeptical.</span></span></layer></div>

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<div style='text-align:left;font-family:"Gill Sans";font-weight:normal;
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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>
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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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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%;
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</i></span></div>

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<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:
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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>
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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>

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<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%;
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style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>3. Can you
exploit literature mining tools to </span></span></layer><script>
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</i></span></span></layer></div>

</layer><script>
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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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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>
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-</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>

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-
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-</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
deleted file mode 100755
index 6b671799..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0062.htm
+++ /dev/null
@@ -1,109 +0,0 @@
-<html>

<head>
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<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
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style='font-size:73%'><i>Contact for comments and improvements:</i></span><span
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</span></div>

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</layer><script>
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<div><script>
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<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>
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style='text-align:left'><span style='font-size:82%'>rwilliam@nb.utmem.edu<br>
</span></span></layer><script>
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<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>

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<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>
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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";
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%;
color:#E9EB5D'>ongoing study of R. Wiliams and R. Homayouni (July 15, 2005)</span><span
style='font-family:"Gill Sans";font-size:300%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><br>
</span></span></layer></div>

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</layer>

<script language=JavaScript><!--

-//-->

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\ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0063.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0063.htm
deleted file mode 100755
index 0c358615..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0063.htm
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@@ -1,34 +0,0 @@
-<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
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<script>
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0064.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0064.htm
deleted file mode 100755
index 49a071a3..00000000
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@@ -1,34 +0,0 @@
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<meta name=ProgId content=PowerPoint.Slide>
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<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_collapsed.htm
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
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<body bgcolor=black text=white link=white vlink=white alink=white
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<table  width=100%>
 <tr>
  <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID1 VISIBILITY=hidden >&gt;</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>
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<table  width=100%>
 <tr>
  <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID2 VISIBILITY=hidden >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p2" ><font face=Arial size=2><b><a
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  href="javascript:parent.base.Slide('3')" id=AREF>Slide 3</a></b></font></td>
 </tr>
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 <tr>
  <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID4 VISIBILITY=hidden >&gt;</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>
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<table  width=100%>
 <tr>
  <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID5 VISIBILITY=hidden >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p5" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('5')" id=AREF>&quot;First page of data:&quot;</a></b></font></td>
 </tr>
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  <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID6 VISIBILITY=hidden >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p6" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('6')" id=AREF>&quot;Data sources:&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p7" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('7')" id=AREF>&quot;Expression estimates
  for App on...&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p8" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('8')" id=AREF>&quot;Critiquing the App
  data the...&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p9" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('9')" id=AREF>&quot;App expression after
  windsorizing&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p10" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('10')" id=AREF>&quot;Discovering shared
  expression patterns&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p11" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('11')" id=AREF>&quot;Transcript
  neighborhoods&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p12" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('12')" id=AREF>&quot;App and Atcay
  transcript scatterplot&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p13" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('13')" id=AREF>&quot;App transcript and
  eight of...&quot;</a></b></font></td>
 </tr>
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<table  width=100%>
 <tr>
  <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID14 VISIBILITY=hidden >&gt;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p15" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('15')" id=AREF>&quot;Correlations of App
  with classical...&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p16" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('16')" id=AREF>&quot;Network Graph of App
  with...&quot;</a></b></font></td>
 </tr>
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<table  width=100%>
 <tr>
  <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID17 VISIBILITY=hidden >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p17" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('17')" id=AREF>&quot;Summary of Part 1:&quot;</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 >&gt;</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
deleted file mode 100755
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_expand.gif
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diff --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
deleted file mode 100755
index a45e9c0c..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_expanded.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">
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href="webqtl_demo2_part1.ppt.ppt">
<script>
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-	window.location.replace( "endshow.htm" );
-}
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<meta name=Robots content=NoIndex>
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<!--a {text-decoration: none;}-->
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</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 >&gt;</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&#8211;16)</font></td>
 </tr>
 <tr>
  <td colspan=1></td>
  <td colspan=1><font face=Arial size=2>Part 2. Discovering upstream modulators
  (slides 17&#8211;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 >&gt;</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>
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  <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID3 VISIBILITY=hidden >&gt;</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>

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 <tr>
  <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID4 VISIBILITY=hidden >&gt;</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 >&gt;</ilayer>'); } </script></td>
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  href="javascript:parent.base.Slide('5')" id=AREF>&quot;First page of data:&quot;</a></b></font></td>
 </tr>
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  <td width=5 nowrap></td>
  <td width="100%"></td>
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  <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>
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<br>

<table  width=100%>
 <tr>
  <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID6 VISIBILITY=hidden >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p6" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('6')" id=AREF>&quot;Data sources:&quot;</a></b></font></td>
 </tr>
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 <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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p7" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('7')" id=AREF>&quot;Expression estimates
  for App on...&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p8" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('8')" id=AREF>&quot;Critiquing the App
  data the...&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p9" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('9')" id=AREF>&quot;App expression after
  windsorizing&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p10" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('10')" id=AREF>&quot;Discovering shared
  expression patterns&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p11" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('11')" id=AREF>&quot;Transcript
  neighborhoods&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p12" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('12')" id=AREF>&quot;App and Atcay
  transcript scatterplot&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p13" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('13')" id=AREF>&quot;App transcript and
  eight of...&quot;</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 >&gt;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p15" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('15')" id=AREF>&quot;Correlations of App
  with classical...&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p16" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('16')" id=AREF>&quot;Network Graph of App
  with...&quot;</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 >&gt;</ilayer>'); } </script></td>
  <td width=100%  id="p17" ><font face=Arial size=2><b><a
  href="javascript:parent.base.Slide('17')" id=AREF>&quot;Summary of Part 1:&quot;</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 >&gt;</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
deleted file mode 100755
index f47a3707..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_navigation_bar.htm
+++ /dev/null
@@ -1,37 +0,0 @@
-<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();
-}
-
-function writebody() {
-
-	if ( parent.g_showoutline ) {
-			document.write('<table border=0 valign=top cellspacing=0 width=\"100%\">' + 
-			'<tr valign=top><td align=left valign=top>' );
-			  document.write( '<a href=\"javascript:parent.ToggleOutline()\" ><img src=\"outline.gif\" title=\"Show/Hide Outline\" alt=\"Show/Hide Outline\" border=0></a>' );
-			  document.write( '</td>' );
-		if( parent.g_outline_href == parent.OUTLINE_EXPAND_HREF ) {
-			document.write( '<td align=right valign=top><a href=\"javascript:parent.CollapseOutline()\">' +
-			'<img src="outline_collapse.gif" title="Collapse Outline" alt="Collapse Outline" border=0>' +  
-			'</a></td>');
-		} else {
-			document.write('<td align=right valign=top><a href=\"javascript:parent.ExpandOutline()\">' +
-			'<img src="outline_expand.gif" title="Expand Outline" alt="Expand Outline" border=0>' + 
-			 '</a></td>');
-		}
-		document.write("</tr></table>");
-	}
-	else {
-			document.write( '<table border=0 valign=top cellspacing=0 width=\"100%\"><td align=\"left\"><a href=\"javascript:parent.ToggleOutline()\" ><img border=0 src=\"outline.gif\" title=\"Show/Hide Outline\" alt=\"Show/Hide Outline\"></a></td></table>' );
-	}
-}//-->

-</script>
</head>

<body background=navbg.gif topmargin=1 onresize="restore()" scroll="no" >
<script language=JavaScript><!--

-writebody();
-//-->

-</script>
</body>

</html>
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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
deleted file mode 100755
index 004a872f..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/prev_active.gif
+++ /dev/null
diff --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
deleted file mode 100755
index 8a467185..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/prev_disabled.gif
+++ /dev/null
diff --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
deleted file mode 100755
index 7c9fb703..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/script.js
+++ /dev/null
@@ -1,1351 +0,0 @@
-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( " > &nbsp " + 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 ) {
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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
deleted file mode 100755
index d17c2490..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001.htm
+++ /dev/null
@@ -1,25 +0,0 @@
-<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>
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<meta name=Description content="Aug-15-05: GeneNetwork and WebQTL:">
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<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&#8211;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&#8211;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><!--

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-
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-</script>
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\ No newline at end of file
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+++ /dev/null
@@ -1,5 +0,0 @@
-<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 ) {
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</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
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002.htm
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@@ -1,25 +0,0 @@
-<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>
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<meta name=Description content=Aug-15-05>
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<style media=print>
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<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
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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">&nbsp; </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">&nbsp; </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">&nbsp;
  </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">&nbsp;&nbsp; </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">&nbsp; </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
deleted file mode 100755
index 2eb797be..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image002.png
+++ /dev/null
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deleted file mode 100755
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image003.png
+++ /dev/null
diff --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
deleted file mode 100755
index a4f088b8..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image004.png
+++ /dev/null
diff --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
deleted file mode 100755
index 5f7740c5..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp; </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">&nbsp;
  </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">&nbsp;&nbsp; </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">&nbsp; </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
deleted file mode 100755
index 5507bd68..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003.htm
+++ /dev/null
@@ -1,25 +0,0 @@
-<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>
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<meta name=Description content=Aug-15-05>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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	width:6.0in !important;
	height:4.5in !important;
	font-size:76% !important;}
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</style>
<script language=JavaScript src=script.js></script><script language=JavaScript><!--

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-</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
deleted file mode 100755
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image005.png
+++ /dev/null
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+++ /dev/null
diff --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
deleted file mode 100755
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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>
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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
deleted file mode 100755
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004.htm
+++ /dev/null
@@ -1,25 +0,0 @@
-<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>
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<script language=JavaScript src=script.js></script><script language=JavaScript><!--

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</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">&nbsp; </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">&nbsp; </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
deleted file mode 100755
index 08c136e3..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image010.png
+++ /dev/null
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image012.png
+++ /dev/null
diff --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
deleted file mode 100755
index f7336dcc..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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>
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-	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">&nbsp; </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">&nbsp; </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>
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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
deleted file mode 100755
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005.htm
+++ /dev/null
@@ -1,25 +0,0 @@
-<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"
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-var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1;
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-</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
deleted file mode 100755
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image013.png
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deleted file mode 100755
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image014.png
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diff --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
deleted file mode 100755
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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>
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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
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006.htm
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@@ -1,25 +0,0 @@
-<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;}
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</style>
<script language=JavaScript src=script.js></script><script language=JavaScript><!--

-gId="slide0006.htm"
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-var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1;
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-</script><script for=window event=onload language=JavaScript><!--

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-LoadSld( gId );
-playList();MakeSldVis(1);
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</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
deleted file mode 100755
index ff7d776a..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_image015.png
+++ /dev/null
diff --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
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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" );
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</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>
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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
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-<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;
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<script language=JavaScript src=script.js></script><script language=JavaScript><!--

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-LoadSld( gId );
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-</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">&nbsp;&nbsp; </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>
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+++ /dev/null
@@ -1,5 +0,0 @@
-<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>
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</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>
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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
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<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>
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<script>
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-	window.location.replace( "endshow.htm" );
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<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;
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</style>
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<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>

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\ 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
deleted file mode 100755
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diff --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
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deleted file mode 100755
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">
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<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>
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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
deleted file mode 100755
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-<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>
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<meta name=Description content=Aug-15-05>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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<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() {
-
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-</script>
</body>

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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
deleted file mode 100755
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009_image022.png
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+++ /dev/null
@@ -1,5 +0,0 @@
-<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">
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href="webqtl_demo2_part1.ppt.ppt">
<script>
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<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>
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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
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-<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>
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-	window.location.replace( "endshow.htm" );
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<meta name=Description content=Aug-15-05>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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	{left:0px !important;
	width:6.0in !important;
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<script language=JavaScript src=script.js></script><script language=JavaScript><!--

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</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%);
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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>
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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
deleted file mode 100755
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_image023.png
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+++ /dev/null
@@ -1,5 +0,0 @@
-<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>
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-<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>
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<meta name=Description content=Aug-15-05>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
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<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><!--

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-//-->

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</body>

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@@ -1,5 +0,0 @@
-<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>
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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
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<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>
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<meta name=Description content=Aug-15-05>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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	{left:0px !important;
	width:6.0in !important;
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<script language=JavaScript src=script.js></script><script language=JavaScript><!--

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</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() {
-
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-//-->

-</script>
</body>

</html>
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@@ -1,5 +0,0 @@
-<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">
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<script>
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<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>
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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
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<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>
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<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;
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<script language=JavaScript src=script.js></script><script language=JavaScript><!--

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<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%);
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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>
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-<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">
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</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>
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-<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>
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<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
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<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">&nbsp;
  </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
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+++ /dev/null
@@ -1,5 +0,0 @@
-<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">&nbsp;
  </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>
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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
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-<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>
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<meta name=Description content=Aug-15-05>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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</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>
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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
deleted file mode 100755
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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>
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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
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@@ -1,25 +0,0 @@
-<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" );
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<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;
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<script language=JavaScript src=script.js></script><script language=JavaScript><!--

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</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%);
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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>
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-<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>
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<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>

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<head>
<meta http-equiv=Content-Type content="text/html; charset=macintosh">
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<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
genomics</title>
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href="webqtl_demo2_part1.ppt.ppt">
<script>
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<meta name=Description content=Aug-15-05>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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<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">&nbsp;</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">&nbsp;</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">&nbsp;</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">&nbsp;</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">&nbsp;</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">&nbsp;</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">&nbsp;</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>

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<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>
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<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%);
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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'>

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  <td width="100%"></td>
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<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
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</i></span></div>

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color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
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upstream </span></span></layer><script>
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style='text-align:left'><span style='font-size:106%;color:#E9EB5D;mso-color-index:
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mso-color-index:3;mso-special-format:lastCR;display:none'><br>
</span></span></layer></div>

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<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%;
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display:none'><br>
</span></div>

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<div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
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</span></div>

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<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>
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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>
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-</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>

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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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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>

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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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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>

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<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>

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<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>

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</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>
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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
deleted file mode 100755
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0019_notes_pane.htm
+++ /dev/null
@@ -1,5 +0,0 @@
-<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">
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<body bgcolor=black text=white>

<table border=0 width="100%">
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  <td width="100%"></td>
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 <tr>
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  <td align=left colspan=1><font face=Verdana size=2>END</font><br>
  </td>
 </tr>
</table>

</body>

</html>
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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
deleted file mode 100755
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0020.htm
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@@ -1,172 +0,0 @@
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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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<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>

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<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>
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<div><script>
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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%;
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<div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
mso-color-index:3'>Enter<br>
</span></div>

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<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>

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<div><script>
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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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<div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
mso-color-index:3'>Select<br>
</span></div>

</layer><script>
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<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>

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<div><script>
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<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%;
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</layer>

<layer>
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 mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%;
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</layer>

<layer>
 <div style='text-align:left;font-family:"Gill Sans";font-weight:normal;
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 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>
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-</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>

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<div><script>
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<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>
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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">&nbsp;
</span></span></span></layer><script>
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%;
color:#E9EB5D;mso-color-index:3'>species, </span></span></layer><script>
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color:#E9EB5D;mso-color-index:3'>and type</span></span></layer></div>

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</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">&nbsp;
   </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">&nbsp;
   </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">&nbsp;&nbsp; </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">&nbsp; </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><!--

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<layer>
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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>

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   <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>
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   <td align=left colspan=1><font face=Helvetica size=3>RESULTS OF THE APP
   SEARCH.<span style="mso-spacerun: yes">&nbsp; </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>
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  <tr>
   <td colspan=1></td>
   <td align=left colspan=1><font face=Helvetica size=3>1. APP is a great
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   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
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   and the 3Õ untranslated region (UTR) of the amyloid precursor protein (APP).<span
   style="mso-spacerun: yes">&nbsp; </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>
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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
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0023.htm
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</i></span></div>

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<div><span style='font-size:200%;color:#E9EB5D'><i>about<br>
</i></span></div>

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<div><span style='font-size:200%;color:#E9EB5D'><i>data<br>
</i></span></div>

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<div><span style='font-size:200%;color:#E9EB5D'><i>source</i></span></div>

</layer></div>

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  <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>
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<script language=JavaScript><!--

-//-->

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</html>
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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
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0024.htm
+++ /dev/null
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<head>
<meta name=ProgId content=PowerPoint.Slide>
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<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
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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>

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   <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>
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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
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--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0025.htm
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<head>
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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>

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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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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>
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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">&nbsp;&nbsp; </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>

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-

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   <td align=left colspan=1><font face=Helvetica size=3>This slide shows you
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   first set of BXD strains</font><br>
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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
deleted file mode 100755
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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
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display:none'><br>
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:150%;
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:150%;
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suspiciously low. BXD5 is noisy. </span><span style='font-family:"Gill Sans";
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</span></span></layer></div>

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   <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>
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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
deleted file mode 100755
index 0a23d59d..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0027.htm
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display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
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windsorizing</span></div>

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   <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
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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
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display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
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  </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>
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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
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  </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>
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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>

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   <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>
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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
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its neighbors</span></div>

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  <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>
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\ 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
deleted file mode 100755
index 85ee47fe..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0032.htm
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mso-text-raise:0%'><span style='font-size:82%'><i>App</i></span><span
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style='mso-special-format:lastCR;display:none'><br>
</span></div>

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-

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 <div id=NotesObj style='display:none'>
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  <tr>
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   <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">&nbsp;
   </span>Size of 16 by 16 inches; Gene Symbols; Don't Show Correlations; Use
   curved lines (aka ÒedgesÓ).</font><br>
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\ 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
deleted file mode 100755
index 042ca4ad..00000000
--- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0033.htm
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@@ -1,104 +0,0 @@
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style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span
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 <div id=NotesObj style='display:none'>
 <table style='color:white' border=0 width="100%">
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   <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>
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-//-->

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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
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<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;
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font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt:
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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>

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   <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>
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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
deleted file mode 100755
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<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;
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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>

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<layer>
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</layer>

<layer>
 <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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</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>
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<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>
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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">&nbsp;</span>You have learned the basics
about searching for traits<br>
</span></span></layer></div>

</layer><script>
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<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>
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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">&nbsp;</span>You know some methods to check
data quality<br>
</span></span></layer></div>

</layer><script>
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<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 + ' >' );
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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">&nbsp;</span>You know how to edit bad or
suspicious data<br>
</span></span></layer></div>

</layer><script>
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<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">&nbsp;</span>You know how to review the
basic statistics of a trait<br>
</span></span></layer></div>

</layer><script>
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<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>
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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">&nbsp;</span>You know how to generate a
scattergram between two </span></span></layer><script>
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-</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>
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<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>
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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">&nbsp;</span>You know how to add items to
your SELECTIONS window<br>
</span></span></layer></div>

</layer><script>
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<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>
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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;
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font-size:200%;color:#E9EB5D'> findings reviewed in this presentation are part
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diff --git a/web/tutorial/ppt/index.html b/web/tutorial/ppt/index.html
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--- a/web/tutorial/ppt/index.html
+++ /dev/null
@@ -1,90 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
-<HTML><HEAD><TITLE>Powerpoint / GeneNetwork</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>
-</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 width="100%" height=200 bgColor=#eeeeee>
-		<P class="title">GeneNetwork PowerPoint Demonstrations  <A HREF="/webqtl/WebQTL.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A></P>
-		<blockquote>
-			<P class="subtitle">GeneNetwork Demonstration Part I </P>
-
-<P>Part I: A short introduction on <B>how to exploit GeneNetwork to explore variation and covariation among traits</B>. 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. 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
-	//-->
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-</BODY>
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