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<!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>
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