UCSC Stem Cell Genomics Heatmap <LINK REL="STYLESHEET" HREF="../style/HGStyle.css" TYPE="text/css"> <LINK REL="STYLESHEET" HREF="hgHeatmapStyle.css" TYPE="text/css"> </head> <BODY BACKGROUND="/images/floret.jpg" LINK="#0000CC" VLINK="#330066" ALINK="#6600FF"><A NAME="TOP"></A> <TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH="100%">  <TD COLSPAN=2 height=40> <TABLE BGCOLOR="#000000" CELLPADDING=1 CELLSPACING=1 WIDTH="100%" HEIGHT="27"> <TR BGCOLOR="#2636D1"><TD VALIGN="middle"> <TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 BGCOLOR="#2636D1" HEIGHT="24"> <TR><TD VALIGN="middle"><FONT COLOR="#89A1DE"> <A HREF="/index.html" class="topbar">Home</A> - <A HREF="/hgHeatmap" class="topbar">Stem Cell Genomics</A> - <A HREF="/cgi-bin/hgGateway" class="topbar">Genomes</A> - <A HREF="/stemCellGenomics/help/userGuide/userGuide.html" class="topbar">Help</A> </FONT></TD></TR> </TABLE> </TD></TR> </TABLE> </TD>  <TR><TD COLSPAN=3>  <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"><TR><TD> <TABLE BGCOLOR="#FFFEE8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"><TR><TD> <TABLE BGCOLOR="#D9E4F8" BACKGROUND="../images/hr.gif" WIDTH="100%"> <TR><TD> <FONT SIZE="4"><b> UCSC Stem Cell Genomics Heatmaps</b></FONT> </TD></TR></TABLE> <TABLE BACKGROUND="/images/floret.jpg" BGCOLOR="#FFFEE8" WIDTH="100%" CELLPADDING=0><TR><TH HEIGHT=10></TH></TR> <TR><TD WIDTH=10> </TD><TD>  <div id='error' style="text-align:center; background: white; color: red; display: none; font-size: small; border: 1px red dashed;"> <span style="font-size: large;">Sorry, an error has occurred!</span><br>Generally, a <a href="javascript: location.reload(true);">refresh</a> will solve any problems you're having.<br> If you continue to experience issues, please contact <a href="mailto:genome-cancer@soe.ucsc.edu">genome-cancer@soe.ucsc.edu</a> with the following information:<br> <pre id='errorMsg'> </pre> If you would like to hide this message and try to continue anyway, click <a href="javascript: void(0);" onclick="$('#error').hide();">here</a>. </div> <div id='devWarning' style="text-align:center; background: yellow; color: black; font-size: small; display: none;"> <em>Disclaimer</em>: The UCSC Stem Cell Genomics Browser is still under heavy development and QA. There may be features that are broken and data that are wrong. We are attempting to stabilize and verify the cancer browser as quickly as possible. Please be patient, and be sure to <a href="mailto:genome-cancer@soe.ucsc.edu">let us know</a> of any issues you experience. <br> Feel free to click <a href="javascript: void(0);" onclick="$('#devWarning').hide();">here</a> to hide this message. </div> <div id='videoTutorial' style="text-align:center; width: 500px; margin: auto; border: 1px black solid; background: #2636D1; color: white; font-size: small; "> Need help? Check out our <a href='http://genome-cancer.ucsc.edu/cancerGenomics/tutorial/' target="_blank" style='color: white;'>video tutorial</a> and follow along! </div> <table id='heatmapTable' class="heatmapTable">  </table> <div id='tooltip'></div> <div id='featureControls'> <div id='featureControlsSlider' class='ui-slider' style="margin-left: 10px;"> <div class='ui-slider-handle'></div> <div class='ui-slider-handle' style="left: 188px;"></div> </div> </div> <div id='dragHelper'> </div> <p></p> <form name='datasetsForm' id='datasetsForm' onsubmit="function(){return false;};" action="javascript: void(0);"> <table id='datasetsOuterTable' style="width: 80%; margin: auto;"> <tbody> <tr class="heatmapControlHeader clickme" onclick='$("#datasetsDisplayOptions").toggle();'><th>Display Options</th></tr> <tr> <td> <table class="heatmapDatasetControlLabel" style="width:100%;" id='datasetsDisplayOptions'> <tbody> <tr style='font-weight: bold;'> <td>Display As</td> <td>Heatmap Click</td> <td>Update Display Settings</td> </tr> <tr> <td><select name='dsDisplayAs' id='dsDisplayAs' onchange='$(".dsConfigureDisplayCell").toggle(); if($(this).val() == "geneset") $("#hmClick").val("sort"); updateAllDatasets();'><option value='chrom'>Chromosomes</option><option value='geneset'>Genesets</option></select></td> <td><select name='hmClick' id='hmClick'><option value='zoom'>Zooms (chrom only)</option><option value='sort'>Sorts</option></select></td> <td><input type='button' value='update' name='updateDisplayButton' id='updateDisplayButton' onclick='updateAllDatasets();'></td> </tr> </tbody> <tbody id='dsConfigureChromDisplayCell' class='dsConfigureDisplayCell' style='display:none;'> <tr > <td colspan='1'>Position: <input type='text' id='chromPos' size='30' onkeypress="positionKeyPress(event)"> <span id='chromPosSize'></span></td> <td colspan='2' style='vertical-align: middle;'><input type='button' id='viewInGenomeBrowser' value='Click to view this region in the UCSC Genome Browser' onclick='viewRegionInGenomeBrowser();' disabled></td> </tr> <tr > <td colspan='1'>RefSeq Gene Track: <select id='refGene' class='hiddenText' onchange='updateAnnotationTrack();'><option value='hide'>Hide</option><option value='show'>Show</option></select></td> <td colspan='2'> </td> </tr> </tbody> <tbody id='dsConfigureGSDisplayCell' class='dsConfigureDisplayCell' style='display:none;'> <tr><td colspan='3'> <table style="width:100%;" cellspacing='0px'> <tr style='font-weight: bold;'>  <td colspan='2' id='dsConfigureGSDisplayCellTabHeader' style='width: 300px; vertical-align: bottom;'> <ul> <li><a href="#existingGenesets-1"><span>Existing Genesets</span></a></li> <li><a href="#userGenesets-2"><span>Create Geneset by Gene Search</span></a></li> <li><a href="#userGenesetList-3"><span>Create Geneset by Gene List</span></a></li> </ul> </td> <td style=' padding-top: 5px; width: 250px; vertical-align: center;'>DISPLAY</td> </td> <tr> <td style='padding-right: 25px; background: #d9e4f8; border: 1px solid #536ED3;' colspan='2'> <table style='width: 100%;' id="existingGenesets-1"> <tr > <td style='width: 300px;'> Search by <select name='geneSearchType' id='geneSearchType'><option value='geneset'>geneset</option><option value='gene'>gene</option></select> name: <input type='text' id='searchGenesetsInput' size='10'> <div class='geneSearchResultDiv'> <ol id='geneSearchResultOL' class='hghList ui-sortable asmListSortable'> </ol> </div> </td> <td style='width: 200px;'> <div class='heatmapControlHeader' id='genesetSearchGenesetName' style='text-align: center; margin-top: 10px;'> </div> <div class='genesetSearchResultDiv' style='margin: auto;'> <ol id='genesetSearchGeneList' class='hghList' style='text-align:center;'> </ol> </div>  </td> </tr> </table> <table style='width: 100%;' id="userGenesets-2"> <tr > <td style='width: 300px;'> Search genes by name: <input type='text' id='searchGenesInput' size='10'> <div class='userGeneSearchResultDiv'> <ol id='userGeneSearchResultOL' class='hghList ui-sortable asmListSortable'> </ol> </div> </td> <td style='width: 200px;'> <div class='heatmapControlHeader' id='userGenesetSearchGenesetName' style='text-align: center;'> Name your geneset:<br/><input type='text' id='userGenesetSearchGeneListuserGenesetName' name='userGenesetSearchGeneListuserGenesetName'><br/> </div> <div class='userGenesetSearchResultDiv' style='margin: auto;'> <ol id='userGenesetSearchGeneList' class='hghList' style='text-align:center;'> </ol> </div> <div id='addGeneset' style='text-align: center; display: none;' onclick='saveUserGeneset("userGenesetSearchGeneList");'><span class='addGeneset'>save & add geneset</span></div> </td> </tr> </table> <table style='width: 100%;' id="userGenesetList-3"> <tr > <td style='width: 300px;'> <textarea name='userGenesetListTextarea' id='userGenesetListTextarea' rows='10' cols='30'></textarea> <input type='button' value='Validate & Add -->' onclick='userGenesetListValidate();'> </td> <td style='width: 200px;'> <div class='heatmapControlHeader' id='userGenesetListSearchGenesetName' style='text-align: center;'> Name your geneset:<br/><input type='text' id='userGenesetListSearchGeneListuserGenesetName' name='userGenesetListSearchGeneListuserGenesetName'><br/> </div> <div class='userGenesetListSearchResultDiv' style='margin: auto;'> <ol id='userGenesetListSearchGeneList' class='hghList' style='text-align:center;'> </ol> </div> <div id='addUserGenesetList' style='text-align: center; display: none;' onclick='saveUserGeneset("userGenesetListSearchGeneList");'><span class='addGeneset'>save & add geneset</span></div> </td> </tr> </table> </td> <td id='geneSearchDisplayCell'> <ol id='geneSearchDisplayOL' class='hghList ui-sortable asmListSortable'> <li class='hghListItem'><span class='hghListItemLabel' geneset="GO:0000082">GO:0000082</span><a href='javascript:void(0);' class='hghListItemRemove' onclick='$(this).parent("li").remove();'><img src='close.gif'></a></li> </ol> </td> </tr> </table> </td></tr> </tbody> </table> </td> </tr> <tr class="heatmapControlHeader clickme" onclick='$("#datasetsInnerTable").toggle();'><th>Datasets</th></tr> <tr> <td> <table class="heatmapDatasetControlLabel" style="width:100%;" id='datasetsInnerTable'> <tbody id='datasetsInnerTableBody'> </tbody> <tbody id='datasetsInnerTableBodyPrivate'> <tr class='heatmapControlHeader clickme' id='datasetLoginPromptHeader'><th colspan='5' onclick='$("#datasetLoginPrompt").toggle();'>Private (click to login)</th></tr> <tr id='datasetLoginPrompt' style='display: none;'><td colspan='5'><div style='display: none; color:red;' id='incorrectLogin'>The username or password was incorrect.</div><div>Username: <input type='text' name='username' id='username'><br>Password: <input type='password' name='rawPassword' id='rawPassword'><br><input type='button' value='Submit' onclick='login();' id='loginSubmit'></div></td></tr> </tbody> </table> </tr> </tbody> </table> </form> <p> </p> <div align='center' > <div style="background: white; margin: auto; width: 300px; border-width: 1px 5px 5px 1px; border-color: #536ED3; border-style: solid;"> <strong>Save / Load Current Layout</strong><br/> <input type='text' id='shareUrl' size='15'> <br/> <input type='button' onclick='save();' value='save'> <input type='button' onclick='load();' value='load'> </div> </div>  </TD><TD WIDTH=15></TD></TR></TABLE> </TD></TR></TABLE> </TD></TR></TABLE> </TD></TR></TABLE> </BODY></HTML>