2ab662767ea06905eb431182ac306c37f9a606e8 kate Mon Dec 17 18:51:32 2018 -0800 Initial draft of GTEx static page. refs #22678 diff --git src/hg/htdocs/gtex.html src/hg/htdocs/gtex.html new file mode 100755 index 0000000..47bbe8a --- /dev/null +++ src/hg/htdocs/gtex.html @@ -0,0 +1,84 @@ +<!DOCTYPE html> +<!--#set var="TITLE" value="GTEx Resources at UCSC" --> +<!--#set var="ROOT" value="." --> + +<!--#include virtual="$ROOT/inc/gbPageStart.html"--> + +<link rel="stylesheet" href="<!--#echo var="ROOT" -->/style/hgGtexTrackSettings.css"> + +<h1>Genotype Tissue Expression (GTEx) Project Resources at UCSC</h1> +<p> +The <a href="https://commonfund.nih.gov/gtex" target="_blank">Genotype Tissue Expression +(GTEx) Project</a> is a data resource and tissue bank established by the +<a target="_blank" href="https://commonfund.nih.gov/about">National Institutes of Health Common Fund</a>, +in order to study the relationship between genetic variation and gene expression in +a variety of human tissues. A total of 53 tissues from nearly 1000 individuals have been studied +by genomic and RNA sequencing. These resources are valuable for exploring the genetic basis of +human diseases.</p> +<p> +The UCSC Genome Browser provides visualization resources for selected summary data from the GTEx project. +More extensive data access and visualizations are available from the +<a target="_blank" href="https://gtexportal.org">GTEx Portal</a>, a resource provided by the +GTEx Laboratory, Data Analysis and Coordinating Center at the Broad Institute.</p> + +<div class="row"> + <div class="col-md-6"> + <h2>GTEx Tissue Body Map</h2> +<p>This interactive graphic identifies the tissues sampled by GTEx for gene expression studies. +Some GTEx browser tracks include the Body Map in the track configuration page, to facilitate +limiting track display to tissues of interest. A stand-alone page with the interactive +graphic is <a target="_blank" href="../gtexBodyMap.html">here</a>.</p> + +<!-- + <a target="_blank" href="../gtexBodyMap.html"><img src="../images/gtexBodyMap.svg" alt="GTEx Body Map"> +--> + <p class="text-center"> + <object id="bodyMapSvg" type="image/svg+xml" + data="<!--#echo var="ROOT" -->/images/gtexBodyMapPage.svg"></object> + <!--<div class="gbmCredit">Credit: jwestdesign</div> --> + </p> + </div> + <div class="col-md-6"> + <div class="row"> + <h2>GTEx data at UCSC</h2> + <ul> + <li><a target="_blank" + href="../cgi-bin/hgGtexTrackSettings?db=hg19&g=gtexGene#INFO_SECTION"> + GTEx Gene track</a></li> + <li><a target="_blank" + href="../cgi-bin/hgGtexTrackSettings?db=hg19&g=gtexTranscExpr#INFO_SECTION"> + GTEx Transcript track</a></li> + <li><a target="_blank" + href="../cgi-bin/hgTrackUi?db=hg19&g=gtexEqtlCluster#TRACK_HTML"> + GTEx Combined eQTL track</a></li> + <li><a target="_blank" + href="../cgi-bin/hgTrackUi?db=hg19&g=gtexEqtlTissue#TRACK_HTML"> + GTEx Tissue eQTL track</a></li> + <li><a target="_blank" + href="http://hgdownload.soe.ucsc.edu/hubs/gtex/gtexHub.html"> + GTEx Signal hub</a></li> + <li><a target="_blank" + href="http://hgdownload.soe.ucsc.edu/hubs/gtexAnalysis/gtexAnalysisHub.html"> + GTEx Analysis hub</a></li> + </ul> + </div> + <div class="row"> + <h2>GTEx in the browser</h2> + <p> +Below is a screenshot of a +<a target="_blank" +href="http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=kate&hgS_otherUserSessionName=GTEx%20demo%20for%20blog"> +public session</a> + that highlights the GTEx gene expression track and GTEx RNA-seq signal hub for the <a target="_blank" href="http://genome.ucsc.edu/blog/gtex-resources-in-the-browser/">GTEx Resources in the Genome Browser blog article</a>. +The session shows a genomic region where 5 genes exhibit different patterns of tissue-specific expression. + <p class="text-center"> + <img src="../images/gtexBlogSession.png" width="540px" height="424px"></p> + </div> + </div> +</div> + +<!--#include virtual="$ROOT/inc/gbPageEnd.html"--> + +<script type='text/javascript' src='/js/hgGtexTrackSettings.js'></script> + +