anchor.diff:  <script type="text/javascript" src="${pageContext.request.contextPath}/scripts/feedback.js"></script>
   <script type="text/javascript" src="${pageContext.request.contextPath}/scripts/jquery.tablesorter.min.js"></script>
   <script type="text/javascript" src="${pageContext.request.contextPath}/scripts/common-query.js"></script>
  -<script language="javascript" type="text/javascript" src="${pageContext.request.contextPath}/scripts/jquery.flot.atlas.js"></script>
  -
  -<link rel="stylesheet" href="${pageContext.request.contextPath}/atlas.css" type="text/css" />
  -<link rel="stylesheet" href="${pageContext.request.contextPath}/geneView.css" type="text/css" />
  +<script language="javascript" type="text/javascript"
  +        src="${pageContext.request.contextPath}/scripts/jquery.flot.atlas.js"></script>
  +
  +<link rel="stylesheet" href="${pageContext.request.contextPath}/atlas.css" type="text/css"/>
  +<link rel="stylesheet" href="${pageContext.request.contextPath}/geneView.css" type="text/css"/>
   
   
   <script type="text/javascript">
   
  -    function showThumbTooltip(x, y, contents) {
  -        if(contents != 'Mean'){
  -            $('<div id="tooltip" />').text(contents).css( {
  -                position: 'absolute',
  -                display: 'none',
  -                top: (y+5)+'px',
  -                left: (x+5)+'px',
  -                border: '1px solid #005555',
  -                margin: '0px',
  -                backgroundColor: '#EEF5F5'
  -            }).appendTo("body").fadeIn('fast');
  -        }
  +function showThumbTooltip(x, y, contents) {
  +    if (contents != 'Mean') {
  +        $('<div id="tooltip" />').text(contents).css({
  +            position: 'absolute',
  +            display: 'none',
  +            top: (y + 5) + 'px',
  +            left: (x + 5) + 'px',
  +            border: '1px solid #005555',
  +            margin: '0px',
  +            backgroundColor: '#EEF5F5'
  +        }).appendTo("body").fadeIn('fast');
       }
  -
  -    function drawPlot(jsonObj, plot_id){
  -        if(jsonObj.series){
  -            var legend_id = plot_id.replace("_plot", "_legend");
  -            jsonObj.options.legend.container = '#' + legend_id;
  -            var plot = $.plot($('#'+plot_id), jsonObj.series, jsonObj.options);
  -
  -            var previousPoint = null;
  -            $('#'+plot_id).bind("plothover", function (event, pos, item) {
  -                if (item) {
  -                    if (previousPoint != item.datapoint) {
  -                        previousPoint = item.datapoint;
  -                        $("#tooltip").remove();
  -                        showThumbTooltip(item.pageX, item.pageY, item.series.label);
  -                    }
  -                }else {
  +}
  +
  +function drawPlot(jsonObj, plot_id) {
  +    if (jsonObj.series) {
  +        var legend_id = plot_id.replace("_plot", "_legend");
  +        jsonObj.options.legend.container = '#' + legend_id;
  +        var plot = $.plot($('#' + plot_id), jsonObj.series, jsonObj.options);
  +
  +        var previousPoint = null;
  +        $('#' + plot_id).bind("plothover", function (event, pos, item) {
  +            if (item) {
  +                if (previousPoint != item.datapoint) {
  +                    previousPoint = item.datapoint;
                       $("#tooltip").remove();
  -                    previousPoint = null;
  +                    showThumbTooltip(item.pageX, item.pageY, item.series.label);
                   }
  -            });
  -            return plot;
  -        }
  -        return null;
  -    }
  -
  -    function drawPlots(){
  -        $(".plot").each(function(){
  -            var plot_id = this.id;
  -            var tokens = plot_id.split('_');
  -            var eid = tokens[0];
  -            var gid = tokens[1];
  -            atlas.ajaxCall("plot", { gid: gid, eid: eid, plot: 'bar' }, function(o){
  -                drawPlot(o,plot_id);
  -            });
  -        });
  -    }
  -
  -    function redrawPlotForFactor(eid,gid,ef,mark,efv){
  -        var plot_id = eid+"_"+gid+"_plot";
  -        atlas.ajaxCall("plot", { gid: gid, eid: eid, ef: ef, plot: 'bar' }, function(o){
  -                var plot = drawPlot(o,plot_id);
  -                if(mark){
  -                    markClicked(eid, gid, ef, efv, plot, o);
  -                }
  -        });
  -        drawEFpagination(eid,gid,ef);
  -    }
  -
  -    function drawEFpagination(eid,gid,currentEF,plotType) {
  -        var panelContent = [];
  -
  -        $("#"+eid+"_EFpagination *").each(function(){
  -            var ef = $(this).attr("id");
  -            var ef_txt = $(this).html();
  -            if(ef == currentEF){
  -                panelContent.push("<span id='"+ef+"' class='current'>"+ef_txt+"</span>")
  -            }
  -            else{
  -                panelContent.push('<a id="'+ef+'" onclick="redrawPlotForFactor( \''+eid+'\',\''+gid+'\',\''+ef+'\',\''+plotType+'\',false)">'+ef_txt+'</a>');
  +            } else {
  +                $("#tooltip").remove();
  +                previousPoint = null;
               }
           });
  -
  -        $("#"+eid+"_EFpagination").empty();
  -        $("#"+eid+"_EFpagination").html(panelContent.join(""));
  +        return plot;
       }
  -
  -
  -    function markClicked(eid,gid,ef,efv,plot,jsonObj) {
  -
  -        var plot_id = eid+'_'+gid+'_plot';
  -        var allSeries = plot.getData();
  -        var series;
  -        var markColor;
  -
  -        for (var i = 0; i < allSeries.length; ++i){
  -            if(allSeries[i].label){
  -                if(allSeries[i].label.toLowerCase()==efv.toLowerCase()){
  -                    series = allSeries[i];
  -                    markColor = series.color;
  -                    break;
  -                }
  -            }
  +    return null;
  +}
  +
  +function drawPlots() {
  +    $(".plot").each(function() {
  +        var plot_id = this.id;
  +        var tokens = plot_id.split('_');
  +        var eid = tokens[0];
  +        var gid = tokens[1];
  +        atlas.ajaxCall("plot", { gid: gid, eid: eid, plot: 'bar' }, function(o) {
  +            drawPlot(o, plot_id);
  +        });
  +    });
  +}
  +
  +function redrawPlotForFactor(eid, gid, ef, mark, efv) {
  +    var plot_id = eid + "_" + gid + "_plot";
  +    atlas.ajaxCall("plot", { gid: gid, eid: eid, ef: ef, plot: 'bar' }, function(o) {
  +        var plot = drawPlot(o, plot_id);
  +        if (mark) {
  +            markClicked(eid, gid, ef, efv, plot, o);
           }
  -
  -        if(series==null){
  -            return ;
  +    });
  +    drawEFpagination(eid, gid, ef);
  +}
  +
  +function drawEFpagination(eid, gid, currentEF, plotType) {
  +    var panelContent = [];
  +
  +    $("#" + eid + "_EFpagination *").each(function() {
  +        var ef = $(this).attr("id");
  +        var ef_txt = $(this).html();
  +        if (ef == currentEF) {
  +            panelContent.push("<span id='" + ef + "' class='current'>" + ef_txt + "</span>")
           }
  -
  -        var data = series.data;
  -        var xMin= data[0][0]
  -        var xMax= data[data.length-1][0]
  -
  -        var overviewDiv = $('#'+plot_id+'_thm');
  -        if(allSeries.length>10 && data.length<5){
  -            if(overviewDiv.height()!=0){
  -                var overview = $.plot($('#'+plot_id+'_thm'), jsonObj.series, jsonObj.options);
  -
  -                overview.setSelection({ xaxis: { from: xMin-10, to: xMax+10 }});
  -            }
  -            plot = $.plot($('#'+plot_id), jsonObj.series,$.extend(true, {}, jsonObj.options, {
  -                grid:{ backgroundColor: '#fafafa',	autoHighlight: true, hoverable: true, borderWidth: 1, markings: [{ xaxis: { from: xMin-1, to: xMax+1 }, color: '#FFFFCC' }]},
  -                xaxis: { min: xMin-10, max: xMax+10  }, yaxis: {labelWidth:40}
  -            }));
  +        else {
  +            panelContent.push('<a id="' + ef + '" onclick="redrawPlotForFactor( \'' + eid + '\',\'' + gid + '\',\'' + ef + '\',\'' + plotType + '\',false)">' + ef_txt + '</a>');
           }
  -        else{
  -
  -            plot = $.plot($('#'+plot_id), jsonObj.series, $.extend(true, {}, jsonObj.options, {
  -                grid:{ backgroundColor: '#fafafa',	autoHighlight: true, hoverable: true, borderWidth: 1, markings: [{ xaxis: { from: xMin-1, to: xMax+1 }, color: '#FFFFCC' }]},
  -                yaxis: {labelWidth:40}
  -            }));
  -            if(overviewDiv.height() != 0) {
  -                var overview = $.plot($('#'+plot_id+'_thm'), jsonObj.series,$.extend(true,{},jsonObj.options,{color:['#999999','#D3D3D3']}));
  -
  -                overview.setSelection({ xaxis: { from: xMin-10, to: xMax+10 }});
  +    });
  +
  +    $("#" + eid + "_EFpagination").empty();
  +    $("#" + eid + "_EFpagination").html(panelContent.join(""));
  +}
  +
  +
  +function markClicked(eid, gid, ef, efv, plot, jsonObj) {
  +
  +    var plot_id = eid + '_' + gid + '_plot';
  +    var allSeries = plot.getData();
  +    var series;
  +    var markColor;
  +
  +    for (var i = 0; i < allSeries.length; ++i) {
  +        if (allSeries[i].label) {
  +            if (allSeries[i].label.toLowerCase() == efv.toLowerCase()) {
  +                series = allSeries[i];
  +                markColor = series.color;
  +                break;
               }
           }
       }
   
  -
  -    function reloadExps(){
  -
  -        $('#ExperimentResult').load("${pageContext.request.contextPath}/geneExpList",{gid:${atlasGene.geneId},from:"1", to:"5"},drawPlots);
  -        $('#pagingSummary').empty();
  -        $(".heatmap_over").removeClass("heatmap_over");
  -        paginateExperiments();
  -        countExperiments();
  -	}
  -
  -    function countExperiments(){
  -       $("#pagingSummary").text("${noAtlasExps} experiment${noAtlasExps>1?'s':''} showing differential expression");  
  +    if (series == null) {
  +        return;
       }
   
  -    function paginateExperiments(){
  -         // Create pagination element
  -         <c:if test="${noAtlasExps > 5}">
  -        	$("#Pagination").pagination(${noAtlasExps}, {
  -				num_edge_entries: 2,
  -				num_display_entries: 5,
  -				items_per_page:5,
  -                callback: pageselectCallback
  -         	});
  -         </c:if>
  +    var data = series.data;
  +    var xMin = data[0][0]
  +    var xMax = data[data.length - 1][0]
  +
  +    var overviewDiv = $('#' + plot_id + '_thm');
  +    if (allSeries.length > 10 && data.length < 5) {
  +        if (overviewDiv.height() != 0) {
  +            var overview = $.plot($('#' + plot_id + '_thm'), jsonObj.series, jsonObj.options);
  +
  +            overview.setSelection({ xaxis: { from: xMin - 10, to: xMax + 10 }});
  +        }
  +        plot = $.plot($('#' + plot_id), jsonObj.series, $.extend(true, {}, jsonObj.options, {
  +            grid:{ backgroundColor: '#fafafa',    autoHighlight: true, hoverable: true, borderWidth: 1, markings: [
  +                { xaxis: { from: xMin - 1, to: xMax + 1 }, color: '#FFFFCC' }
  +            ]},
  +            xaxis: { min: xMin - 10, max: xMax + 10  }, yaxis: {labelWidth:40}
  +        }));
       }
  -
  -	function pageselectCallback(page_id){
  -		var fromPage = (page_id*5) +1;
  -		var toPage = (page_id*5) + 5;
  -		$('#ExperimentResult').load("${pageContext.request.contextPath}/geneExpList",{gid:${atlasGene.geneId},from:fromPage, to: toPage},drawPlots);
  -	}
  -
  -
  -	function FilterExps(el,fv,ef){
  -
  -        $('#ExperimentResult').empty();                            
  -
  -		$('#ExperimentResult').load("${pageContext.request.contextPath}/geneExpList",{gid:${atlasGene.geneId}, efv: fv, factor:ef},
  -							function(){
  -								for (var i = 0; i < exps.length; ++i){
  -									var eid = jQuery.trim(exps[i].id);
  -									redrawPlotForFactor(eid,'${atlasGene.geneId}',ef,true,fv);
  -								}
  -								$('#pagingSummary').text(exps.length+" experiment"+(exps.length>1?"s":'')+" showing differential expression in \""+ fv + "\"");
  -								var lnk = $("<a>Show all studies</a>").bind("click", reloadExps);
  -								$("#Pagination").empty().append(lnk);
  -							});
  -
  -
  -        old = $(".heatmap_over");
  -		old.removeClass("heatmap_over");
  -        old.addClass ("heatmap_row");
  -		el.className = "heatmap_over";
  -		//window.scrollTo(0,0);
  -	}
  -
  -
  -    function FilterExpsEfo(el,efo){
  -        $('#ExperimentResult').empty();
  -        $('#ExperimentResult').load("${pageContext.request.contextPath}/geneExpList",{gid:${atlasGene.geneId}, efo: efo},
  -                            function(){
  -                                for (var i = 0; i < exps.length; ++i){
  -                                    var eid = jQuery.trim(exps[i].id);
  -                                    redrawPlotForFactor(eid,'${atlasGene.geneId}','organismpart',true,'');
  -                                }
  -                                $('#pagingSummary').text(exps.length+" experiment"+(exps.length>1?"s":'')+" showing differential expression in \""+ efo + "\"");
  -                                var lnk = $("<a>Show all studies</a>").bind("click", reloadExps);
  -                                $("#Pagination").empty().append(lnk);
  -                            });
  -        old = $(".heatmap_over");
  -        old.removeClass("heatmap_over");
  -        old.addClass ("heatmap_row");
  -        el.className = "heatmap_over";
  -        //window.scrollTo(0,0);
  +    else {
  +
  +        plot = $.plot($('#' + plot_id), jsonObj.series, $.extend(true, {}, jsonObj.options, {
  +            grid:{ backgroundColor: '#fafafa',    autoHighlight: true, hoverable: true, borderWidth: 1, markings: [
  +                { xaxis: { from: xMin - 1, to: xMax + 1 }, color: '#FFFFCC' }
  +            ]},
  +            yaxis: {labelWidth:40}
  +        }));
  +        if (overviewDiv.height() != 0) {
  +            var overview = $.plot($('#' + plot_id + '_thm'), jsonObj.series, $.extend(true, {}, jsonObj.options, {color:['#999999','#D3D3D3']}));
  +
  +            overview.setSelection({ xaxis: { from: xMin - 10, to: xMax + 10 }});
  +        }
       }
  -
  -    jQuery(document).ready(function()
  -    {
  -        countExperiments();
  -        paginateExperiments();
  -        $("#heatmap_tbl").tablesorter({
  -            headers: {2: {sorter: false}}});
  -        drawPlots();
  +}
  +
  +
  +function reloadExps() {
  +
  +    $('#ExperimentResult').load("${pageContext.request.contextPath}/geneExpList", {gid:${atlasGene.geneId},from:"1", to:"5"}, drawPlots);
  +    $('#pagingSummary').empty();
  +    $(".heatmap_over").removeClass("heatmap_over");
  +    paginateExperiments();
  +    countExperiments();
  +}
  +
  +function countExperiments() {
  +    $("#pagingSummary").text("${noAtlasExps} experiment${noAtlasExps>1?'s':''} showing differential expression");
  +}
  +
  +function paginateExperiments() {
  +    // Create pagination element
  +<c:if test="${noAtlasExps > 5}">
  +    $("#Pagination").pagination(${noAtlasExps}, {
  +        num_edge_entries: 2,
  +        num_display_entries: 5,
  +        items_per_page:5,
  +        callback: pageselectCallback
       });
  +</c:if>
  +}
  +
  +function pageselectCallback(page_id) {
  +    var fromPage = (page_id * 5) + 1;
  +    var toPage = (page_id * 5) + 5;
  +    $('#ExperimentResult').load("${pageContext.request.contextPath}/geneExpList", {gid:${atlasGene.geneId},from:fromPage, to: toPage}, drawPlots);
  +}
  +
  +
  +function FilterExps(el, fv, ef) {
  +
  +    $('#ExperimentResult').empty();
  +
  +    $('#ExperimentResult').load("${pageContext.request.contextPath}/geneExpList", {gid:${atlasGene.geneId}, efv: fv, factor:ef},
  +            function() {
  +                for (var i = 0; i < exps.length; ++i) {
  +                    var eid = jQuery.trim(exps[i].id);
  +                    redrawPlotForFactor(eid, '${atlasGene.geneId}', ef, true, fv);
  +                }
  +                $('#pagingSummary').text(exps.length + " experiment" + (exps.length > 1 ? "s" : '') + " showing differential expression in \"" + fv + "\"");
  +                var lnk = $("<a>Show all studies</a>").bind("click", reloadExps);
  +                $("#Pagination").empty().append(lnk);
  +            });
  +
  +
  +    old = $(".heatmap_over");
  +    old.removeClass("heatmap_over");
  +    old.addClass("heatmap_row");
  +    el.className = "heatmap_over";
  +    //window.scrollTo(0,0);
  +}
  +
  +
  +function FilterExpsEfo(el, efo) {
  +    $('#ExperimentResult').empty();
  +    $('#ExperimentResult').load("${pageContext.request.contextPath}/geneExpList", {gid:${atlasGene.geneId}, efo: efo},
  +            function() {
  +                for (var i = 0; i < exps.length; ++i) {
  +                    var eid = jQuery.trim(exps[i].id);
  +                    redrawPlotForFactor(eid, '${atlasGene.geneId}', 'organismpart', true, '');
  +                }
  +                $('#pagingSummary').text(exps.length + " experiment" + (exps.length > 1 ? "s" : '') + " showing differential expression in \"" + efo + "\"");
  +                var lnk = $("<a>Show all studies</a>").bind("click", reloadExps);
  +                $("#Pagination").empty().append(lnk);
  +            });
  +    old = $(".heatmap_over");
  +    old.removeClass("heatmap_over");
  +    old.addClass("heatmap_row");
  +    el.className = "heatmap_over";
  +    //window.scrollTo(0,0);
  +}
  +
  +jQuery(document).ready(function()
  +{
  +    countExperiments();
  +    paginateExperiments();
  +    $("#heatmap_tbl").tablesorter({
  +        headers: {2: {sorter: false}}});
  +    drawPlots();
  +});
   </script>
   
   
  -<link rel="stylesheet" href="${pageContext.request.contextPath}/blue/style.css" type="text/css" media="print, projection, screen" />
  -<link rel="stylesheet" href="${pageContext.request.contextPath}/structured-query.css" type="text/css" />
  +<link rel="stylesheet" href="${pageContext.request.contextPath}/blue/style.css" type="text/css"
  +      media="print, projection, screen"/>
  +<link rel="stylesheet" href="${pageContext.request.contextPath}/structured-query.css" type="text/css"/>
   ${atlasProperties.htmlBodyStart}
   
   <div class="contents" id="contents">
  
positive.code:   ~ http://gxa.github.com/gxa
    --%>
  
  <c:set var="timeStart" value="${u:currentTime()}" />
  
  <u:htmlTemplate file="look/genePage.head.html" />
  
  <meta name="Description" content="${atlasGene.geneName} (${atlasGene.geneSpecies}) - Gene Expression Atlas Summary"/>
  <meta name="Keywords" content="ArrayExpress, Atlas, Microarray, Condition, Tissue Specific, Expression, Transcriptomics, Genomics, cDNA Arrays" />
  
  <jsp:include page="../includes/query-includes.jsp"/>
  <!--[if IE]><script language="javascript" type="text/javascript" src="${pageContext.request.contextPath}/scripts/excanvas.min.js"></script><![endif]-->
  
negative.code: 
  
  <table cellspacing="0" cellpadding="0" border="0" width="100%">
      <tr>
          <td style="vertical-align:top;">
              <table width="100%" style="background-color: white" class="geneAnnotations">
  
                  <tr>
                      <td align="left" class="geneName">${atlasGene.geneName}
                          <div style="font:normal"><c:import url="../includes/apilinks.jsp"><c:param name="apiUrl"
                                                                                                     value="geneIs=${atlasGene.geneIdentifier}"/></c:import></div>
                      </td>
                      <td style="vertical-align: text-bottom">${atlasGene.geneSpecies}</td>
                      <td rowspan="">
  
                      </td>
                  </tr>
  
                  <tr>
                      <td colspan="2" align="left" style="padding-bottom:1em;padding-top:1em">
                          ${f:escapeXml(atlasGeneDescription)}
                      </td>
                  </tr>
  
  
                  <c:set var="synonyms">
                      <c:forEach items="${atlasProperties.geneAutocompleteNameFields}" var="prop" varStatus="s"><c:if
                              test="${!empty atlasGene.geneProperties[prop]}">${u:join(atlasGene.geneProperties[prop], ", ")}
                          <c:if test="${!s.last}">, </c:if></c:if></c:forEach>
                  </c:set>
                  <c:if test="${!empty synonyms}">
                      <tr>
                          <td class="geneAnnotHeader">Synonyms</td>
                          <td align="left">${synonyms}</td>
                      </tr>
                  </c:if>
  
                  <c:if test="${!empty orthologs}">
                      <tr>
                          <td class="geneAnnotHeader">Orthologs</td>
  
                          <td align="left">
                              <c:set var="orthoIds" value=""/>
                              <c:forEach var="ortholog" items="${orthologs}">
                                  <a href="${pageContext.request.contextPath}/gene/${ortholog.geneIdentifier}"
                                     target="_self"
                                     title="Gene Atlas Data For ${ortholog.geneName} (${ortholog.geneSpecies})">${ortholog.geneName}
                                      (${ortholog.geneSpecies})</a>&nbsp;
                                  <c:set var="orthoIds" value="${orthoIds}${ortholog.geneIdentifier}+"/>
                              </c:forEach>
                              (<a href="${pageContext.request.contextPath}/qrs?gprop_0=&gval_0=${orthoIds}${atlasGene.geneIdentifier}&fexp_0=UP_DOWN&fact_0=&specie_0=&fval_0=(all+conditions)&view=hm"
                                  target="_self">Compare orthologs</a>)
                          </td>
                      </tr>
                  </c:if>
  
                  <c:forEach items="${atlasGene.genePropertiesIterator}" var="prop">
                      <c:if test="${!u:isIn(atlasProperties.geneAutocompleteNameFields, prop) && !u:isIn(atlasProperties.genePageIgnoreFields, prop)}">
                          <tr class="${u:isIn(atlasProperties.genePageDefaultFields, prop) ? '' : 'expandable'}"
                              style="${u:isIn(atlasProperties.genePageDefaultFields, prop) ? '' : 'display:none'}">
                              <td class="geneAnnotHeader">${f:escapeXml(atlasProperties.curatedGeneProperties[prop])}</td>
                              <td align="left">
                                  <c:choose>
                                      <c:when test="${!empty atlasProperties.genePropertyLinks[prop]}">
                                          <c:forEach items="${atlasGene.geneProperties[prop]}" var="v" varStatus="s">
                                              <a href="${f:replace(atlasProperties.genePropertyLinks[prop], '$$', v)}"
                                                 target="_blank">${f:escapeXml(v)}</a><c:if test="${!s.last}">, </c:if>
                                          </c:forEach>
                                      </c:when>
                                      <c:otherwise>
                                          ${u:limitedJoin(atlasGene.geneProperties[prop], 5, ", ", "...")}
                                      </c:otherwise>
                                  </c:choose>
                              </td>
                          </tr>
                      </c:if>
                  </c:forEach>
  
                  <tr>
                      <td class="geneAnnotHeader">Search EB-eye</td>
                      <td align="left">
                          <a title="Show gene annotation" target="_blank"
                             href="http://www.ebi.ac.uk/ebisearch/search.ebi?db=genomes&t=${atlasGene.geneIdentifier}">
                              ${atlasGene.geneIdentifier}
                          </a>
                      </td>
  
                      <!-- td width="8%">&nbsp;</td-->
  
                  </tr>
  
                  <tr>
                      <td colspan="2" style="padding-top:5px">
                          <a href="#"
                             onclick="javascript:$(this).parents('table:first').find('.expandable').show();$(this).remove();return false;"><img
                                  src="${pageContext.request.contextPath}/images/expp.gif" alt="" border="none"> Show more
                              properties</a>
                      </td>
                  </tr>
              </table>
          </td>
          <td style="padding-top:15px;">
              <c:if test="${atlasGene.hasAnatomogram}">
                  <!--
                  <img src="${pageContext.request.contextPath}/anatomogram/${atlasGene.geneIdentifier}.png" alt="anatomogram" border="1px" />
                  -->
              </c:if>
          </td>
      </tr>
  </table>
  
  <table cellspacing="0" cellpadding="0" style="margin-top:40px">
  
  
  <tr>
  <td>
  <table cellspacing="0" cellpadding="0" border="0">
  <tr>
  <td valign="top" width="50%">
  <table>
  <tr>
      <td class="sectionHeader" style="padding-right:20px;">
  
  
          <c:choose>
              <c:when test="${ef!=null}">
                  ${f:escapeXml(atlasProperties.curatedEfs[ef])}
                  <div style="font-size:10px; font-weight:normal;"><a
                          href="${pageContext.request.contextPath}/gene/${atlasGene.geneIdentifier}">&lt;&lt;view all
                      experimental factors</a></div>
              </c:when>
              <c:otherwise>
                  Experimental Factors
              </c:otherwise>
          </c:choose>
  
      </td>
  </tr>
  
  <tr>
  <td style="padding-top: 3px; width:60%;">
  
  <table cellpadding="0" style="width:100%;" border="0">
      <tr>
  
          <c:forEach var="experimentalFactor" items="${differentiallyExpressedFactors}" varStatus="i" end="5">
          <c:if test="${(i.index mod 2)==0}">
      </tr>
      <tr>
          </c:if>
  
          <td style="vertical-align:top; padding-right:20px;">
              <c:if test="${ef==null}">
                  <div class="geneAnnotHeader"
                       style="width:200px;">${f:escapeXml(atlasProperties.curatedEfs[experimentalFactor.name])}</div>
              </c:if>
              studied in
              <c:forEach var="experiment" items="${experimentalFactor.experiments}" varStatus="i_e">
                  <c:if test="${(i_e.index<5)||(ef!=null)}">
                      <a href="${pageContext.request.contextPath}/experiment/${experiment}/${atlasGene.geneIdentifier}"
                         title="${experiment}">${experiment}</a><c:if test="${!i_e.last}">, </c:if>
                  </c:if>
                  <c:if test="${i_e.last}">
                      <c:if test="${(i_e.count>=5)&&(ef==null)}">
                          ... (${i_e.count} experiments)
                      </c:if>
                  </c:if>
              </c:forEach>
  
              <c:if test='${experimentalFactor.name=="organismpart" && atlasGene.hasAnatomogram}'>
                  <br/>
  
                  <div style="overflow:hidden; <c:if test="${ef==null}">width:300px;</c:if>">
                      <img src="${pageContext.request.contextPath}/<c:if test="${ef==null}">web</c:if>anatomogram/${atlasGene.geneIdentifier}.png"
                           alt="anatomogram" border="none" usemap="#anatomogram"/>
                  </div>
                  <!--
                  <map name="anatomogram">
                  <c:forEach var="anatomogramArea" items="${anatomogramMap}">
                      <area shape="rect"
                      coords="${anatomogramArea.x0},${anatomogramArea.y0},${anatomogramArea.x1},${anatomogramArea.y1}"
                      alt="${anatomogramArea.efo}"
                      href="/${anatomogramArea.efo}.html"
                      onclick="FilterExpsEfo(this,'${u:escapeJS(anatomogramArea.efo)}'); return false;">
  
                  </c:forEach>
                  </map>
                  -->
  
                  <!--
                  <c:forEach var="anatomogramArea" items="${anatomogramMap}">
                      "${anatomogramArea.efo}"
                  </c:forEach>
                  -->
  
                  <c:if test="${ef==null}">
                      <div style="padding-left:0px; font-size:10px;">
                          <a href="${pageContext.request.contextPath}/gene/${atlasGene.geneIdentifier}?ef=${experimentalFactor.name}">show
                              this factor only&gt;&gt;</a>
                      </div>
                  </c:if>
  
              </c:if>
              <c:if test='${experimentalFactor.name!="organismpart" || !atlasGene.hasAnatomogram || ef!=null}'>
                  <!--generic ef - the above clause imposes the following rules:
                  1. in multi-experimental factor experiment view:
                  a. ef != 'organismpart' => always show a table
                  b. ef == 'organismpart'
                  - anatomogram exists => show anatomogram
                  - anatomogram doesn't exist => show table
                  2. in single-experimental factor experiment view: (ef != null):
                  a. as 1a
                  b ef == 'organismpart' => show anatomogram (if exists) AND the table
                  -->
  
                  <table class="heatmap" cellpadding="0" cellspacing="0" border="0"
                         style="margin-top:5px; margin-left:0px; width:100%;">
                      <thead>
                      <tr style="height:26px;border-top:1px solid #CDCDCD">
                          <th style="border: 1px solid #CDCDCD;padding: 1px 5px 1px 4px; width:180px;">Factor Value</th>
                          <th style="border-top:1px solid #CDCDCD;border-bottom:1px solid #CDCDCD;border-right:1px solid #CDCDCD;padding: 1px 2px 1px 4px; width:20px;">
                              <span style="font-size:8px">U/D</span></th>
                          <th style="border-top:1px solid #CDCDCD;border-bottom:1px solid #CDCDCD;border-right:1px solid #CDCDCD;padding: 1px 2px 1px 4px;">
                              Experiments
                          </th>
                      </tr>
                      </thead>
                      <tbody>
                      <c:set var="values" value="${experimentalFactor.topValues}"/>
                      <c:if test="${ef!=null}">
                          <c:set var="values" value="${experimentalFactor.values}"/>
                      </c:if>
                      <c:forEach var="e" items="${values}" varStatus="i">
                          <tr class="heatmap_row"
                              onclick="FilterExps(this,'${u:escapeJS(e.efv)}','${u:escapeJS(e.ef)}'); return false;"
                              title="${atlasGene.geneName}">
                              <td style="padding: 1px 5px 1px 4px;border-bottom:1px solid #CDCDCD; min-width: 100px;border-left:1px solid #CDCDCD;">
                                                                      <span style="font-weight: bold">
                                                                              ${u:truncate(u:upcaseFirst(e.efv), 30)}
                                                                      </span>
                              </td>
  
                              <c:set var="ud" value="${e.payload}"/>
                              <c:choose>
                                  <c:when test="${empty ud || ud.ups + ud.downs + ud.nones == 0}">
                                      <td class="counter"><c:choose><c:when test="${j.first}">
                                          <div class="osq"></div>
                                      </c:when></c:choose></td>
                                  </c:when>
                                  <c:when test="${ud.ups == 0 && ud.downs == 0 && ud.nones > 0}">
                                      <td class="acounter" style="color:black;"
                                          title="in ${f:escapeXml(e.efv)} (${f:escapeXml(e.ef)}) is non-differentially in ${ud.nones} experiment(s)."
                                              >
                                          <div class="osq">${ud.nones}</div>
                                      </td>
                                  </c:when>
                                  <c:when test="${ud.ups > 0 && ud.downs == 0 && ud.nones == 0}">
                                      <td class="acounter upback"
                                          title="in ${f:escapeXml(e.efv)} (${f:escapeXml(e.ef)}) is overexpressed in ${ud.ups} experiment(s)."
                                              >
                                          <div class="osq">${ud.ups}</div>
                                      </td>
                                  </c:when>
                                  <c:when test="${ud.ups == 0 && ud.downs > 0 && ud.nones == 0}">
                                      <td class="acounter downback"
                                          title="in ${f:escapeXml(e.efv)} (${f:escapeXml(e.ef)}) is underexpressed in ${ud.downs} experiment(s)."
                                              >
                                          <div class="osq">${ud.downs}</div>
                                      </td>
                                  </c:when>
                                  <c:when test="${ud.ups > 0 && ud.downs == 0 && ud.nones > 0}">
                                      <td class="acounter"
                                          title="in ${f:escapeXml(e.efv)} (${f:escapeXml(e.ef)}) overexpressed in ${ud.ups} and not differentially expressed in ${ud.nones} experiment(s)."
                                              >
                                          <div class="sq">
                                              <div class="nuduo"></div>
                                              <div class="nunoval">${ud.nones}</div>
                                              <div class="nuupval">${ud.ups}</div>
                                          </div>
                                      </td>
                                  </c:when>
                                  <c:when test="${ud.ups == 0 && ud.downs > 0 && ud.nones > 0}">
                                      <td class="acounter"
                                          title="in ${f:escapeXml(e.efv)} (${f:escapeXml(e.ef)}) underexpressed in ${ud.downs} and not differentially expressed in ${ud.nones} experiment(s)."
                                          onclick="atlas.hmc(${i.index},${j.index},event || window.event)">
                                          <div class="sq">
                                              <div class="ndduo"></div>
                                              <div class="ndnoval">${ud.nones}</div>
                                              <div class="nddnval">${ud.downs}</div>
                                          </div>
                                      </td>
                                  </c:when>
                                  <c:when test="${ud.ups > 0 && ud.downs > 0 && ud.nones == 0}">
                                      <td class="acounter"
                                          title="in ${f:escapeXml(e.efv)} (${f:escapeXml(e.ef)}) overexpressed in ${ud.ups} and underexpressed in ${ud.downs} experiment(s)."
                                              >
                                          <div class="sq">
                                              <div class="udduo"></div>
                                              <div class="uddnval">${ud.downs}</div>
                                              <div class="udupval">${ud.ups}</div>
                                          </div>
                                      </td>
                                  </c:when>
                                  <c:otherwise>
                                      <td class="acounter"
                                          title="in ${f:escapeXml(e.efv)} (${f:escapeXml(e.ef)}) overexpressed in ${ud.ups} and underexpressed in ${ud.downs} experiment(s)."
                                              >
                                          <div class="sq">
                                              <div class="tri"></div>
                                              <div class="tdnval">${ud.downs}</div>
                                              <div class="tupval">${ud.ups}</div>
                                              <div class="tnoval">${ud.nones}</div>
                                          </div>
                                      </td>
                                  </c:otherwise>
                              </c:choose>
  
                              <td style="border:1px solid #CDCDCD; padding-left:5px;">
                                                              <span style="font-size:smaller">
                                                              <c:forEach var="experimentID" items="${ud.experiments}"
                                                                         varStatus="i_e">
                                                                  <c:if test="${(i_e.index<5)}">
                                                                      <a href="${pageContext.request.contextPath}/experiment/${experimentalFactor.experimentAccessions[experimentID]}/${atlasGene.geneIdentifier}"
                                                                         onclick="window.location=this.href;"
                                                                         title="${experimentalFactor.experimentAccessions[experimentID]}">${experimentalFactor.experimentAccessions[experimentID]}</a><c:if
                                                                          test="${!i_e.last}">, </c:if>
                                                                  </c:if>
                                                                  <c:if test="${i_e.last}">
                                                                      <c:if test="${(i_e.count>=5)}">
                                                                          ... (${i_e.count} experiments)
                                                                      </c:if>
                                                                  </c:if>
                                                              </c:forEach>
                                                              </span>
                              </td>
  
                          </tr>
                      </c:forEach>
                      </tbody>
                  </table>
  
  
                  <div style="padding-left:0px">
                      <c:if test="${(experimentalFactor.moreValuesCount>0)&&(ef==null)}">
                          ${experimentalFactor.moreValuesCount} more value(s).
                      </c:if>
                      <c:if test="${ef==null}">
                          <div style="font-size:10px;">
                              <a href="${pageContext.request.contextPath}/gene/${atlasGene.geneIdentifier}?ef=${experimentalFactor.name}">show
                                  this factor only&gt;&gt;</a>
                          </div>
                      </c:if>
                  </div>
                  <!--generic ef -->
              </c:if>
  
              <br/><br/>
  
          </td>
          </c:forEach>
  
          <c:forEach var="k" begin="${4 - i.index mod 2}" end="2">
              <td>
  
              </td>
          </c:forEach>
  
  
      </tr>
  </table>
  
  <c:forEach var="experimentalFactor" items="${differentiallyExpressedFactors}" varStatus="i" begin="6">
      <c:if test="${ef==null}">
          <div class="geneAnnotHeader">${f:escapeXml(atlasProperties.curatedEfs[experimentalFactor.name])}</div>
      </c:if>
      studied in
      <c:forEach var="experiment" items="${experimentalFactor.experiments}" varStatus="i_e">
          <c:if test="${(i_e.index<5)||(ef!=null)}">
              <a href="${pageContext.request.contextPath}/experiment/${experiment}/${atlasGene.geneIdentifier}">${experiment}</a><c:if
                  test="${!i_e.last}">, </c:if>
          </c:if>
          <c:if test="${i_e.last}">
              <c:if test="${(i_e.count>=5)&&(ef==null)}">
                  ... (${i_e.count} experiments)
              </c:if>
          </c:if>
      </c:forEach>
      <c:if test="${ef==null}">
          <div style="font-size:10px;">
              <a href="${pageContext.request.contextPath}/gene/${atlasGene.geneIdentifier}?ef=${experimentalFactor.name}">show
                  this factor only&gt;&gt;</a>
          </div>
      </c:if>
      <br/><br/>
  </c:forEach>
  </td>
  </tr>
  </table>
  
  </td>
  <td valign="top" align="left" width="50%">
      <table align="left">
          <tr>
              <td id="expHeader_td" class="sectionHeader" style="vertical-align: top">Expression Profiles</td>
              <td align="right">
                  <div id="Pagination" class="pagination_ie" style="padding-bottom: 3px; padding-top: 3px; "></div>
                  <div id="Pagination1" class="pagination_ie" style="padding-bottom: 3px; padding-top: 3px; ">
                  </div>
              </td>
          </tr>
  
          <tr>
              <td align="left" valign="top" style="border-bottom:1px solid #CDCDCD;padding-bottom:5px">
                  <div id="pagingSummary" class="header"></div>
              </td>
              <td align="right" style="border-bottom:1px solid #CDCDCD;padding-bottom:5px">
                  <div id="expSelect"></div>
              </td>
  
          </tr>
          <tr>
              <td colspan="2">
                  <div id="ExperimentResult">
                      <c:import url="/geneExpList">
                          <c:param name="gid" value="${atlasGene.geneId}"/>
                          <c:param name="from" value="1"/>
                          <c:param name="to" value="5"/>
                      </c:import>
                  </div>
              </td>
          </tr>
      </table>
  
  </td>
  </tr>
  </table>
  <!--
  <div class="sectionHeader">Old School Vertical Heatmap</div>
  <table class="heatmap" cellpadding="0" cellspacing="0" border="0" id ="heatmap_tbl">
                             <thead>
                                 <tr style="height:26px;border-top:1px solid #CDCDCD">
                                     <th style="border: 1px solid #CDCDCD;padding: 1px 5px 1px 4px;">Factor Value</th>
                                     <th style="border-top:1px solid #CDCDCD;border-bottom:1px solid #CDCDCD;border-right:1px solid #CDCDCD;padding-left:4px;padding-top:1px;padding-bottom:1px">Factor</th>
                                     <th style="border-top:1px solid #CDCDCD;border-bottom:1px solid #CDCDCD;border-right:1px solid #CDCDCD;padding: 1px 2px 1px 4px;">E.</th>
                                 </tr>
                                 <tr>
                                     <td valign="top" height="30" align="center" colspan="3" style="border-bottom:1px solid #CDCDCD;background-color:white;border-left:1px solid #CDCDCD;border-right:1px solid #CDCDCD">
                                         Legend: <img style="position:relative;top:6px" src="${pageContext.request.contextPath}/images/legend-sq.png" height="20"/> - number of studies the gene is <span style="color:red;font-weight:bold">up</span>/<span style="color:blue;font-weight:bold">down</span> in
                                     </td>
                                 </tr>
                             </thead>
                             <tbody>
                                 <c:forEach var="e" items="${heatMapRows}" varStatus="i">
                                     <tr class="heatmap_row"
  
                                         onclick="FilterExps(this,'${u:escapeJS(e.efv)}','${u:escapeJS(e.ef)}')"
                                         title="${atlasGene.geneName}">
                                         <td nowrap="true" style="padding: 1px 5px 1px 4px;border-bottom:1px solid #CDCDCD; min-width: 100px;border-left:1px solid #CDCDCD;">
                                             <span style="font-weight: bold">
                                                     ${u:truncate(u:upcaseFirst(e.efv), 30)}
                                             </span>
                                         </td>
  
                                         <td nowrap="true" style="padding: 1px 5px 1px 4px;border-bottom:1px solid #CDCDCD;min-width: 80px;">
                                             ${f:escapeXml(atlasProperties.curatedEfs[e.ef])}
                                         </td>
  
                                         <c:set var="ud" value="${e.payload}"/>
                                         <c:choose>
                                             <c:when test="${empty ud || ud.ups + ud.downs + ud.nones == 0}">
                                                 <td class="counter"><c:choose><c:when test="${j.first}"><div class="osq"></div></c:when></c:choose></td>
                                             </c:when>
                                             <c:when test="${ud.ups == 0 && ud.downs == 0 && ud.nones > 0}">
                                                 <td class="acounter" style="color:black;"
                                                     title="in ${f:escapeXml(e.efv)} (${f:escapeXml(e.ef)}) is non-differentially in ${ud.nones} experiment(s)."
                                                     ><div class="osq">${ud.nones}</div></td>
                                             </c:when>
                                             <c:when test="${ud.ups > 0 && ud.downs == 0 && ud.nones == 0}">
                                                 <td class="acounter upback"
                                                     title="in ${f:escapeXml(e.efv)} (${f:escapeXml(e.ef)}) is overexpressed in ${ud.ups} experiment(s)."
                                                     ><div class="osq">${ud.ups}</div></td>
                                             </c:when>
                                             <c:when test="${ud.ups == 0 && ud.downs > 0 && ud.nones == 0}">
                                                 <td class="acounter downback"
                                                     title="in ${f:escapeXml(e.efv)} (${f:escapeXml(e.ef)}) is underexpressed in ${ud.downs} experiment(s)."
                                                     ><div class="osq">${ud.downs}</div></td>
                                             </c:when>
                                             <c:when test="${ud.ups > 0 && ud.downs == 0 && ud.nones > 0}">
                                                 <td class="acounter"
                                                     title="in ${f:escapeXml(e.efv)} (${f:escapeXml(e.ef)}) overexpressed in ${ud.ups} and not differentially expressed in ${ud.nones} experiment(s)."
                                                     ><div class="sq"><div class="nuduo"></div><div class="nunoval">${ud.nones}</div><div class="nuupval">${ud.ups}</div></div></td>
                                             </c:when>
                                             <c:when test="${ud.ups == 0 && ud.downs > 0 && ud.nones > 0}">
                                                 <td class="acounter"
                                                     title="in ${f:escapeXml(e.efv)} (${f:escapeXml(e.ef)}) underexpressed in ${ud.downs} and not differentially expressed in ${ud.nones} experiment(s)."
                                                     onclick="atlas.hmc(${i.index},${j.index},event || window.event)"><div class="sq"><div class="ndduo"></div><div class="ndnoval">${ud.nones}</div><div class="nddnval">${ud.downs}</div></div></td>
                                             </c:when>
                                             <c:when test="${ud.ups > 0 && ud.downs > 0 && ud.nones == 0}">
                                                 <td class="acounter"
                                                     title="in ${f:escapeXml(e.efv)} (${f:escapeXml(e.ef)}) overexpressed in ${ud.ups} and underexpressed in ${ud.downs} experiment(s)."
                                                     ><div class="sq"><div class="udduo"></div><div class="uddnval">${ud.downs}</div><div class="udupval">${ud.ups}</div></div></td>
                                             </c:when>
                                             <c:otherwise>
                                                 <td class="acounter"
                                                     title="in ${f:escapeXml(e.efv)} (${f:escapeXml(e.ef)}) overexpressed in ${ud.ups} and underexpressed in ${ud.downs} experiment(s)."
                                                     ><div class="sq"><div class="tri"></div><div class="tdnval">${ud.downs}</div><div class="tupval">${ud.ups}</div><div class="tnoval">${ud.nones}</div></div></td>
                                             </c:otherwise>
                                         </c:choose>
                                     </tr>
                                 </c:forEach>
                             </tbody>
                         </table>
  -->
  
  </td>
  </tr>
  
  </table>
  
  
  <c:set var="timeFinish" value="${u:currentTime()}"/>
  <div align="center">Processing time: <c:out value="${(timeFinish - timeStart) / 1000.0}"/> secs.</div>
  
  </div>
  <!-- /id="ae_pagecontainer" -->
  </div>
  <!-- /id="contents" -->
  
  <u:htmlTemplate file="look/footer.html"/>
  </body></html>
  