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diff --git a/web/index.html.20110408 b/web/index.html.20110408 deleted file mode 100755 index bcae525b..00000000 --- a/web/index.html.20110408 +++ /dev/null @@ -1,367 +0,0 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> -<HTML><HEAD> -<TITLE>GeneNetwork Search</TITLE> -<META http-equiv=Content-Type CONTENT ="text/html; charset=iso-8859-1"> -<META NAME="keywords" CONTENT="genetics, bioinformatics, genome, phenome, gene expression, complex trait analysis, gene mapping, SNP, quantitative trait locus QTL, expression eQTL, WebQTL, Traitnet, Traitnetwork, personalized medicine"> -<META NAME="description" CONTENT ="GeneNetwork is a free scientific web resource used to study relationships between differences in genes, environmental factors, phenotypes, and disease risk." > -<META NAME="author" CONTENT ="GeneNetwork developers" > -<META NAME="title" CONTENT ="GeneNetwork Search" > -<META NAME="pages" CONTENT =""> -<META NAME="collection" CONTENT ="" > -<META NAME="geo.placename" CONTENT ="Memphis, TN" > -<META NAME="geo.region" CONTENT="US-TN"> -<LINK REL="apple-touch-icon" href="/images/ipad_icon3.png" /> -<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/dhtml.js"></SCRIPT> -<SCRIPT SRC="javascript/searchtip.js"></SCRIPT> -</HEAD> - - -<BODY bottommargin="2" leftmargin="1" rightmargin="1" topmargin="4" text=#000000 bgColor=#ffffff onload="javascript:initialDatasetSelection();"> - -<TABLE cellSpacing=5 cellPadding=5 width="100%" border=0> - <TBODY> - <!-- TOP BANNER --> - <TR> - <script language="JavaScript" src="/javascript/header.js"></script> - </TR> -<!-- SINGLE LARGE TABLE CELL FOR THE "SELECT RESOURCE AND SEARCH" PANEL --> - - <TR> - <TD bgColor=#eeeeee class="solidBorder"> - <Table width= "100%" cellPadding=12 cellSpacing=5> - <TR> - <TD vAlign=top width="40%" align="left" height=10 bgColor=#eeeeee> - <p style="font-size:18px;font-family:verdana;color:black"><B> Select and Search</B> - <Form METHOD="POST" ACTION="webqtl/main.py" ENCTYPE="multipart/form-data" NAME="SEARCHFORM"> - <TABLE width="100%"> - - <!-- SPECIES SELECTION --> - <TR> - <TD align=right height="35" style="font-size:14px;font-family:verdana;color:black" width="16%"> - <B>Species:</B> - </TD> - - <TD width="3%"> - </TD> - - <TD NOWRAP width="85%" align="left"> - <DIV Id="menu0"> - <Select NAME="species" size=1 id="species" onchange="fillOptions('species');"> - </Select> - </DIV> - </TD> - </TR> - - <!-- GROUP SELECTION --> - - <TR> - <TD align="right" height="35" style="font-size:14px;font-family:verdana;color:black"> - <B>Group:</B> - </TD> - - <TD width="3%"> - </TD> - - <TD NOWRAP width="85%" align="left"> - <DIV Id="menu1"> - <Select NAME="cross" size=1 id="cross" onchange="fillOptions('cross');"> - </Select> - <input type="button" class="button" value=" Info " onCLick="javascript:crossinfo();"> - </DIV> - </TD> - </TR> - - - <!-- TYPE SELECTION --> - - <TR> - <TD align=right height=35 style="font-size:14px;font-family:verdana;color:black"> - <B>Type:</B> - </TD> - - <TD width="3%"> - </TD> - <TD NOWRAP width="85%" align="left"> - <DIV Id="menu2"> - <Select NAME="tissue" size=1 id="tissue" onchange="fillOptions('tissue');"> - </Select> - </DIV> - </TD> - </TR> - - - <!-- DATABASE SELECTION --> - <TR> - <TD align=right height=35 style="font-size:14px;font-family:verdana;color:black"> - <B>Database:</B> - </TD> - - <TD width="3%"> - </TD> - - <TD NOWRAP width="85%" align="left"> - <DIV Id="menu3"> - <Select NAME="database" size=1 id="database"> - </Select> - <input type="button" class="button" value=" Info " onCLick="javascript:databaseinfo();"> - </DIV> - </TD> - </TR> - - <!-- USER HELP --> - <TR> - <TD align=right height=20 width="10%"> - </TD> - <TD width="3%"> - </TD> - - <TD align="left" width="85%"> - <P class="fs12"> Databases marked with <B>**</B> suffix are not public yet. - <BR> Access requires <A HREF="http://www.genenetwork.org/account.html" target="_blank" class="fs14"><small>user login</small></A>.</P> - </TD> - </TR> - - -<!-- GET ANY SEARCH --> - <TR> - <TD align=right height=35 NOWRAP="on" style="font-size:14px;font-family:verdana;color:black" width="10%"> - <B>Get Any:</B> - </TD> - - <TD width="3%"> - </TD> - - <TD NOWRAP width="85%" align="left"> - <input id="tfor" name="ORkeyword" style="width:420px; background-color:white; font-family:verdana; font-size:14px" type="text" maxlength="500"> - </TD> - </TR> - - - -<!-- GET ANY HELP --> - <TR> - <TD align=right height=20 width="10%"> - </TD> - <TD width="3%"> - </TD> - <TD width="85%" align="left"> - <P class="fs12"> Enter terms, genes, ID numbers in the <B>Get Any</B> field. - <BR> Use <B>*</B> or <B>?</B> wildcards (Cyp*a?, synap*). - <BR> Use <B>Combined</B> for terms such as <I>tyrosine kinase</I>.</P> - </TD> - </TR> - - - -<!-- COMBINED SEARCH --> - - <TR> - <TD align=right height=35 NOWRAP="on" STYLE="font-size:14px;font-family:verdana;color:black" width="10%"> - <B>Combined:</B> - </TD> - <TD width="3%"> - </TD> - - <TD NOWRAP width="85%" align="left"> - <input id="tfand" NAME="ANDkeyword" STYLE="width:420px; background-color:white; font-family:verdana; font-size:14px" type="text" maxlength="500"> - <input name="matchwhole" type="hidden" value="ON"> - </TD> - </TR> - - - -<!-- SEARCH, MAKE DEFAULT, ADVANCED SEARCH --> - - <TR ALIGN="center"> - <TD width="3%"> - </TD> - <TD width="3%"> - </TD> - <TD ALIGN="left" HEIGHT="40" COLSPAN=3> - <INPUT id="btsearch" TYPE="Submit" CLASS="button" STYLE="font-size:12px" VALUE=" Search "> - <INPUT TYPE="button" CLASS="button" STYLE="font-size:12px" VALUE=" Make Default " onClick = "setDefault(this.form);"> - <INPUT TYPE="button" CLASS="button" STYLE="font-size:12px" VALUE=" Advanced Search " onClick="javascript:window.open('index3.html', '_self');"> - </TD> - </TR> - </TABLE> - <INPUT TYPE="hidden" NAME="FormID" VALUE="searchResult"> - <INPUT TYPE="hidden" NAME="RISet" VALUE="BXD"> - <SCRIPT SRC="/javascript/selectDatasetMenu.js"></SCRIPT> - </FORM> - </CENTER> - - - - - -<!-- QUICK HELP --> - -<P><LEFT> ______________________________________________________ - -<P STYLE="font-size:13px;font-family:verdana;color:black"><B> - -Quick HELP Examples and </B> -<A HREF="http://www.genenetwork.org/index4.html" target="_blank" class="fs14"><B> - User's Guide</B></A></P> - - -</CENTER style="font-size:12px;font-family:verdana;color:black"> - You can also use advanced commands. Copy these simple examples -<BR> into the <B>Get Any</B> or <B>Combined</B> search fields: -<UL style="font-size:12px;font-family:verdana;color:black"> - -<LI><B><I>POSITION=(chr1 25 30)</I></B> finds genes, markers, or transcripts on chromosome 1 between 25 and 30 Mb. - -<LI><B><I>MEAN=(15 16) LRS=(23 46)</I></B> in the <B>Combined</B> field finds highly expressed genes (15 to 16 log2 units) AND with peak <A HREF="http://www.genenetwork.org/glossary.html#L" target="_blank" class="fs14"><small>LRS</small></A> linkage between 23 and 46. - -<LI><B><I>RIF=mitochondrial</I></B> searches RNA databases for <A HREF="http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank" class="fs14"><small>GeneRIF</small></A> links. - -<LI><B><I>WIKI=nicotine</I></B> searches <A HREF="http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank" class="fs14"><small>GeneWiki</small></A> for genes that you or other users have annotated with the word <I>nicotine</I>. - -<LI><B><I>GO:0045202</I></B> searches for synapse-associated genes listed in the <A HREF="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank" class="fs14"><small>Gene Ontology</small></A>. - -<LI><B><I>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</I> </B><BR> in <B>Combined</B> finds synapse-associated genes with <A HREF="http://www.genenetwork.org/glossary.html#E" target="_blank" class="fs14"><small>cis eQTL</small></A> on Chr 4 from 122 and 155 Mb with LRS scores between 9 and 999. - -<LI><B><I>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</I> </B><BR> in <B>Combined</B> finds diabetes-associated transcripts with peak <A HREF="http://www.genenetwork.org/glossary.html#E" target="_blank" class="fs14"><small>trans eQTLs</small></A> on Chr 2 between 100 and 105 Mb with LRS scores between 9 and 999. - -</UL> -</DIR> - </TD> - <!-- END OF FIND SELECTOR PULL-DOWN PANEL (LEFT SIDE) --> - - - - - -<!-- START OF TOP RIGHT PANEL --> - - -<TD vAlign=top width="40%" bgColor=#FFFFFF> - <p style="font-size:15px;font-family:verdana;color:black"><B>Top New Features</B> </p> - <BLOCKQUOTE> - <p style="font-size:12px;font-family:verdana;color:black"> <A HREF="http://ucscbrowser.genenetwork.org/" target="_blank" class="fs14"><small>RNA-seq and Whole-Genome Sequencing</small></A> data for mouse BXD strains and DBA/2J.</P> - </BLOCKQUOTE> - - <BLOCKQUOTE> - <p style="font-size:12px;font-family:verdana;color:black"> <A HREF="http://galaxy.genenetwork.org/" target="_blank" class="fs14"><small>CITG Open Galaxy Service</small></A>: 200-core cluster at UTHSC for next-gen sequence analysis.</P> - </BLOCKQUOTE> - - - <P>____________________________ - - - - - <p style="font-size:15px;font-family:verdana;color:black"><B>Getting Started</B> </p> - <OL style="font-size:12px;font-family:verdana;color:black"> - <LI>Select <B>Species</B> (or select All) - <LI>Select <B>Group</B> (a specific sample) - <LI>Select <B>Type</B> of data: - <UL> - <LI>Phenotype (traits) - <LI>Genotype (markers) - <LI>Expression (mRNAs) - </UL> - <LI>Select a <B>Database</B> - <LI>Enter search terms in the <B>Get Any</B> or <B>Combined</B> field: words, genes, ID numbers, probes, advanced search commands - <LI>Click on the <B>Search</B> button - <LI>Optional: Use the <B>Make Default</B> button to save your preferences - - </OL> - <P>____________________________ - -<p style="font-size:14px;font-family:verdana;color:black"><B>How to Use GeneNetwork</B> - - <BLOCKQUOTE> - <p style="font-size:12px;font-family:verdana;color:black">Take a 20-40 minute GeneNetwork <A HREF="http://www.genenetwork.org/tutorial/WebQTLTour/" target="_blank" class="fs14"><small>Tour</small></A> that includes screen shots and typical steps in the analysis.</P> - </BLOCKQUOTE> - <BLOCKQUOTE> - <p style="font-size:12px;font-family:verdana;color:black">For information about resources and methods, select the <img src="http://www.genenetwork.org/images/upload/Info.png" alt="INFO" border= 0 valign="middle"> buttons.</P> - - -<p style="font-size:12px;font-family:verdana;color:black">Try the <A HREF="http://proust.uthsc.edu" target="_blank" class="fs14"><small>Test</small></A> site to explore data and features that are being implemented.</P> - - -<p style="font-size:12px;font-family:verdana;color:black">Review the <A HREF="conditionsofUse.html" target="_blank" class="fs14"><small>Conditions</small></A> and <A HREF="statusandContact.html" target="_blank" class="fs14"><small>Contacts</small></A> pages for information on the status of data sets and advice on their use and citation.</P> - - - </BLOCKQUOTE> - - - <p style="font-size:14px;font-family:verdana;color:black"><B>Mirror and Development Sites</B></P> - - <UL> - <LI><A HREF="http://www.genenetwork.org/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Main GN site at UTHSC</A> (main site) - <LI><A HREF="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Australia at the UWA</A> - <LI><A HREF="http://www.sysgen.org.au/bottom.html" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Genome-Centered Systems Genetics at UWA</A> (Morahan and colleagues) - <LI><A HREF="http://gn.genetics.ucla.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">California at UCLA</A> - <LI><A HREF="http://genenetwork.helmholtz-hzi.de/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Germany at the HZI</A> (QTLminer site, Development) - <LI><A HREF="https://genenetwork.hubrecht.eu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Netherlands at the Hubrecht</A> (Development) - <LI><A HREF="http://xzhou3.memphis.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Memphis at the U of M</A> - <LI><A HREF="http://gnat.versailles.inra.fr/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">France at INRA, Versailles</A> (Development) - <LI><A HREF="http://webqtl.bic.nus.edu.sg/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Singapore at the NUS</A> - <LI><A HREF="http://genenetwork.epfl.ch/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Switzerland at the EPFL</A> - <LI><A HREF="http://biopubinfo.zju.edu.cn/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">China at ZJU</A> (no update)</li> - </UL> - - - <p style="font-size:14px;font-family:verdana;color:black"><B>History and Archive</B> - - <BLOCKQUOTE> - <p style="font-size:12px;font-family:verdana;color:black">GeneNetwork's <A HREF="http://artemis.uthsc.edu" target="_blank" class="fs14"><small>Time Machine</small></A> links to earlier versions that correspond to specific publication dates.</P> - </BLOCKQUOTE> - - <!-- EDITOR'S BUTTON --> - <A HREF="/webqtl/main.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0 align="right"></A></P> - </TD> - -<!-- End of "getting started" table row --> - </TR> - </TABLE> - </TD> - </TR> - - <TR> - <TD align=center bgColor=#ddddff class="solidBorder"> - <!-- START OF FOOTER --> - <TABLE width="100%"> - <script language='JavaScript' src='/javascript/footer.js'></script> - </TABLE> - <!--End of footer--> - </TD> - </TR> -</TABLE> -<!-- /Footer --> -<!-- menu script itself. you should not modify this file --> -<script language="JavaScript" src="javascript/menu_new.js"></script> -<!-- items structure. menu hierarchy and links are stored there --> -<script language="JavaScript" src="javascript/menu_items.js"></script> -<!-- files with geometry and styles structures --> -<script language="JavaScript" src="javascript/menu_tpl.js"></script> -<script language="JavaScript"> - <!--// - // Note where menu initialization block is located in HTML document. - 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