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{{Loading|loadingimage=sprites.gif}}<html><script type="text/javascript" src="/5/sstar/rb_js/jquery-1.7.1.min.js"></script>
<script language="javascript" type="text/javascript" src="/5/sstar/rb_js/flot/jquery.flot.js"></script><script language="javascript" type="text/javascript" src="/5/sstar/rb_js/flot/jquery.flot.axislabels.js"></script>
<script type="text/javascript" src="/5/sstar/rb_js/custom/convert.js"></script></html>
<table>
<table>
<tr><th scope="row" align="right" valign="top"> [[Property:Symbol|Symbol]]:</th><td>[[Symbol::{{{Symbol}}}]]</td></tr>
<tr><th scope="row" align="right" valign="top">[[Property:Symbol|Symbol]]:</th><td>{{#if:{{{Symbol}}}|[[Symbol::{{{Symbol}}}]]|NA}}</td></tr>
<tr><th scope="row" align="right" valign="top"> [[Property:Description|Description]]:</th><td>[[description::{{{description}}}]]</td></tr>
<tr><th scope="row" align="right" valign="top">[[Property:Description|Description]]:</th><td>{{#if:{{{description}}}|[[description::{{{description}}}]]|NA}}</td></tr>
<tr><th scope="row" align="right" valign="top">[[Property:Synonyms|Synonyms]]:</th><td>{{#show:{{FULLPAGENAME}}|?Synonyms}}</td></tr>
<tr><th scope="row" align="right" valign="top">[[Property:Synonyms|Synonyms]]:</th><td>{{#switch:{{{Synonyms}}}|- = NA| |#default = {{#show:{{FULLPAGENAME}}|?Synonyms}} }}</td></tr>
<tr><th scope="row" align="right" valign="top">Species:</th><td>{{#set:tax_id={{{tax_id}}}}}{{#switch:{{{tax_id}}}|9606=Human (Homo sapiens)|10090=Mouse (Mus musculus)}}</td></tr>
<tr><th scope="row" align="right" valign="top">Species:</th><td>{{#set:tax_id={{{tax_id}}}}}{{#switch:{{{tax_id}}}|9606=Human (Homo sapiens)|10090=Mouse (Mus musculus)|NA}}</td></tr>
<!--
<!--
<tr><th scope="row" align="right" valign="top">[[Property:tax_id|Tax ID]]:</th><td>[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=[[tax_id::{{{tax_id}}}]]&mode=Info {{{tax_id}}}]</td></tr>
<tr><th scope="row" align="right" valign="top">[[Property:tax_id|Tax ID]]:</th><td>{{#if:{{{tax_id}}}|[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=[[tax_id::{{{tax_id}}}]]&mode=Info {{{tax_id}}}]|NA}}</td></tr>
-->
--><tr><th scope="row" align="right" valign="top">Xrefs:</th><td>{{#if:{{{GeneID}}}|{{GeneExternalRefs|{{{tax_id}}}|{{{chromosome}}}|{{{GeneID}}}|{{{Symbol}}}|{{{Synonyms}}}|{{{dbXrefs}}}}}|NA}}</td></tr>
<tr><th scope="row" align="right" valign="top">External refs:</th><td>[http://www.ncbi.nlm.nih.gov/gene/{{{GeneID}}} EntrezGene:{{{GeneID}}}] {{#show:{{FULLPAGENAME}}|?dbXrefs}}</td></tr>
<tr><th scope="row" align="right" valign="top">Associated motifs:</th><td>{{#ifeq:{{#expr:{{#ask:[[Category:Motif]][[Name::~{{{Symbol}}}]]|?#|format=count}}+{{#ask:[[Category:NonRedundantMotifCluster]][[EntrezGene::~{{{GeneID}}}]]|?#|format=count}} }} | 0 | NA | {{#if:{{#ask:[[Category:Motif]][[Name::~{{{Symbol}}}]]}}| {{#ask:[[Category:Motif]][[Name::~{{{Symbol}}}]]|template=Jasparlogo_genepage|link=none}}|}}
<tr><th scope="row" align="right" valign="top">Associated motifs:</th><td>
<span>{{#arraymap:{{{GeneID}}}|,|$|
{{#ask:[[Category:SwissregulonMotif]][[EntrezGene::{{{GeneID}}}]]
{{NonRedundantMotifRender|$}}
|?name=
}}</span>}} 
|format=template
|template=SwissregulonResult_withSeqLogo
|sep=<br>
}}
</td></tr>
<tr><th scope="row" align="right" valign="top"> TSS regions:</th><td>
{{#ask:[[Category:FFCP]][[EntrezGene::{{{GeneID}}}]]
|?#
|?Short description
|format=ul
|headers=hide
|propsep=
|recordsep=
|link=subject
|titles=hide
|hidegaps=none
|sep=,  
|manysep=;
|headersep=
|offset=
}}  
</td></tr>
</td></tr>
<tr><th scope="row" align="right" valign="top">Transcripton Factor?: </th><td>{{#switch:{{{tf?}}}|yes=[[tf?::Yes]]|[[tf?::No]]}}</td></tr>
</table>
</table>


{{Fontsize|3|TSS regions }}
----
{{#ask:[[FFCP PHASE2:+]][[Category:FFCP]][[EntrezGene::{{{GeneID}}}]]|?Short_description|format=ttable|mainlabel=TSS peak ID|class=ffcp_list stripe cell-border order-column compact|limit=20000}}
<br>
<html>
<html>
<script language="javascript" type="text/javascript">
<script language="javascript" type="text/javascript">
$(document).ready(function() {  
$(document).ready(function() {  
// TSS regions list
$('.ffcp_list').DataTable({
        dom: 'Blfrtip',
        lengthMenu: [[10, 25, 50, -1], [10, 25, 50, "All"]],
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5']
});
// hide-show animation for ucsc genome browser view
// hide-show animation for ucsc genome browser view
$("#ucsc_snap_view").hover(function(){
$("#ucsc_snap_view").hover(function(){
Line 46: Line 40:
});
});
</script>
</script>
</html>
</html><br>
 
{{Fontsize|3|View on UCSC genome browser }}
<h2>View on UCSC genome browser OSC local mirror</h2>
----
<div id="ucsc_snap_view" style="width:750px; height:30px; border-style:solid; border-width:1px; border-color:#aaaaaa;  overflow:auto;">
<div id="ucsc_snap_view" style="width:750px; height:30px; border-style:solid; border-width:1px; border-color:#aaaaaa;  overflow:auto;">
Mouse over to see Genome browser image, Click image to go to Genome browser
Mouse over to see Genome browser image, Click image to go to Genome browser
{{#ucsc_gb_link:{{#replace:{{#ask:[[Category:FFCP]][[Short description::p1@{{{Symbol}}}]][[FFCP PHASE1:+]]|link=none|headers=hide|limit=1|searchlabel=}}|FFCP PHASE1:|}}}}
</div><br>
{{Fontsize|3|TSS expression}}
----
<html>
<script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.min.js"></script>
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/flot/jquery.flot.min.js"></script>
<style type="text/css" title="currentStyle">
@import "/5/sstar/rb_js/html5button/datatables.css";
</style>


{{#ucsc_link:{{#entre_id_pos:{{{GeneID}}}}}|https://fantom5-collaboration.gsc.riken.jp/ucsc/}}
</html>
</div>


== TSS expression ==
{{#ifexpr: {{#ask:[[Category:FFCP]][[EntrezGene::{{{GeneID}}}]]|format=count}} > 0 |
<html>
<html>
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.js"></script>
<style type="text/css">
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script>
.rotate90 {
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/flot/jquery.flot.min.js"></script>
  -webkit-transform: rotate(-90deg);
 
  -moz-transform: rotate(-90deg);
<style type="text/css" title="currentStyle">
-webkit-transform-origin: 6px 18px;
@import "/resource_browser/rb_js/datatables/media/css/jquery.dataTables.css";
-moz-transform-origin: 6px 18px;
@import "/resource_browser/rb_js/datatables/extras/TableTools/media/css/TableTools.css";
width:1px;
}
.highlight { background-color: yellow }
.highlight { background-color: yellow }
.dataTables_scrollHeadInner tr {
</style>
  vertical-align:bottom;
  align:left;
  height:100px;
}
.rotate90 p {
  -webkit-transform: rotate(-90deg);
  -moz-transform: rotate(-90deg); 
  filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=3);
  width:1px
}
</style>
<script type="text/javascript">
<script type="text/javascript">
$(document).ready(function() {
$(document).ready(function() {
     var oTable =  $('.entrezene_explist').dataTable({
    var orderArr;
"sScrollY": "300px",
    if($('#gene_exptable')[0].rows[1].cells.length>1){
"bScrollCollapse": true,
        orderArr = [[1,'desc']];
"iDisplayLength": -1,
    } else {
"aLengthMenu": [[10, 25, 100, -1], [10, 25, 100, "All"]],
        orderArr = [[0,'asc']];
"aoColumnDefs": [ { "asSorting": [ "desc", "asc" ], "aTargets": [ "_all" ] } , { "bSortable": false, "aTargets": [ 0 ] }],
    }
"aaSorting": [[ 1, "desc" ]]
     var oTable =  $('#gene_exptable').DataTable({
                dom: 'Bfrti',
scrollY: "300px",
scrollCollapse: true,
order: orderArr,
                paging: false,
buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
columnDefs: [{ orderSequence: [ "asc", "desc" ], type: "html", targets: [ 0 ] }, { orderSequence: [ "desc", "asc" ], targets: [ "_all" ] } ]
});
});
 
$('#gene_exptable_wrapper .dataTables_scrollHead th').css("height", "100px").css("vertical-align", "bottom");
var oTableTools = new TableTools( oTable, {"sSwfPath": "/resource_browser/rb_js/datatables/extras/TableTools/media/swf/copy_csv_xls_pdf.swf", "aButtons": [ {"sExtends": "copy", "mColumns": "visible"}, {"sExtends": "csv", "mColumns": "visible"}, {"sExtends": "pdf", "mColumns": "visible"} ]});
 
$('#export_tool').before( oTableTools.dom.container );


var data = [];
var data = [];
var plotdata = [];
var plotdata = [];
 
var slist = [];
 
// chart checkbox
// chart checkbox
//$("#test").text("");
for (var i2=1; i2<$('#gene_exptable thead th').length; i2++){
for (var i2=1; i2<$("#dynamic tr")[0].cells.length; i2++){
//var t1 = oTable.fnSettings().aoColumns[i2].sTitle.replace('class="rotate90"', '');
var t1 = oTable.fnSettings().aoColumns[i2].sTitle.replace(/<(?:.|\n)*?>/gm, '').replace(/(^\s+)|(\s+$)/g, "");
 
key2 = i2-1;
key2 = i2-1;
 
         $("#gene_exptable_chart_chkbox").append('<input type="checkbox" name="' + key2 +
         $("#chart_chkbox").append('<input type="checkbox" name="' + key2 +
                               '" checked="checked" id="id' + key2 + '"><label for="id' + key2 + '">'
                               '" checked="checked" id="id' + key2 + '"><label for="id' + key2 + '">'
                                 + t1+ '</label><br/>');
                                 + $('#gene_exptable thead th:nth-child('+(i2+1)+')').text() + '</label><br/>');
//                                + $('.dataTables_scrollHeadInner tr')[0].cells[i2].innerText + '</label>');
}
}
 
$(oTable.settings().column(i2).title).text()
 
 
 
function collectdata(){
function collectdata(){
data = [];
// for (i2=1, len2=oTable.settings().columns.length; i2<len2; i2++){
for (i2=1, len2=$('#gene_exptable thead th').length; i2<len2; i2++){


data = [];
for (var i2=1; i2<$("#dynamic tr")[0].cells.length; i2++){
var plots = [];
var plots = [];
for (var i1=1; i1<$('#dynamic tr').length; i1++) {
for (i1=2, len1=$('#gene_exptable tr').length; i1<len1; i1++) {
     plots.push([i1,$("#dynamic tr")[i1].cells[i2].innerHTML]);
     plots.push([i1,$("#gene_exptable tr")[i1].cells[i2].innerHTML]);
}
}
data.push({"label": oTable.fnSettings().aoColumns[i2].sTitle.replace(/<(?:.|\n)*?>/gm, '').replace(/(^\s+)|(\s+$)/g, ""), "data": plots});
data.push({"label": $('#gene_exptable thead th:nth-child('+(i2+1)+')').text(), "data": plots});
}
}
slist = [];
for (i1=2, len1=$('#gene_exptable tr').length; i1<len1; i1++) {
    slist.push($("#gene_exptable tr")[i1].cells[0].innerHTML);
}
}
}




Line 134: Line 121:
plotdata = [];
plotdata = [];


$("#chart_chkbox").find("input:checked").each(function () {
$("#gene_exptable_chart_chkbox").find("input:checked").each(function () {
var key = $(this).attr("name");
var key = $(this).attr("name");
plotdata.push(data[$(this).attr("name")]);
plotdata.push(data[$(this).attr("name")]);
});
});


var plot1 = $.plot($("#placeholder"), plotdata, {
var plot1 = $.plot($("#gene_exptable_chart"), plotdata, {
                 yaxis : { axisLabel : 'TPM' },
                 yaxis : { axisLabel : 'TPM' },
lines : { show : false },
lines : { show : false },
Line 146: Line 133:
xaxis : { tickDecimals : 0, show: false },
xaxis : { tickDecimals : 0, show: false },
                 legend: { show: false }
                 legend: { show: false }
//                legend: { show: true, container: $("#legends")}
});
});


Line 152: Line 138:
var data_series = plot1.getData();
var data_series = plot1.getData();


$("#chart_chkbox label").css("background-color", "white");
$("#gene_exptable_chart_chkbox label").css("background-color", "white");
 
 
$.each(data_series , function(){
$.each(data_series , function(){
$("#gene_exptable_chart_chkbox label:contains(" + this.label + ")").css("background-color", this.color);
});




$("#chart_chkbox label:contains(" + this.label + ")").css("background-color", this.color);
});
//$('div.rotate90:eq(1)').css("background-color", testseries[0].color);
//$('.dataTables_scrollHeadInner tr:nth-child(2n)').css("background-color", testseries[0].color);
//$('.dataTables_scrollHeadInner tr')[0].cells[1].innerText("text");


}
}


collectdata();
collectdata();
drawchart();
if($('#gene_exptable')[0].rows[1].cells.length>1){
 
    drawchart();
 
}


// re-draw chart event
// re-draw chart event
$(window).resize(function() { drawchart(); });
$(window).resize(function() { drawchart(); });
$("th").click(function() {collectdata(); drawchart(); } );
$("th").click(function() {collectdata(); drawchart(); } );
$("#dynamic_paginate").click(function() {collectdata(); drawchart(); } );
$("#gene_exptable_paginate").click(function() {collectdata(); drawchart(); } );
$('#dynamic').bind('filter', function() {  
$('#gene_exptable').bind('filter', function() {  
setTimeout(function(){
setTimeout(function(){
collectdata(); drawchart();}, 1000);
collectdata(); drawchart();}, 1000);
  } );
  } );
$('#dynamic_length').change(function() {collectdata(); drawchart(); } );
$('#gene_exptable_length').change(function() {collectdata(); drawchart(); } );
 
$("#gene_exptable_chart_chkbox").find("input").click(function() { drawchart(); });
$("#chart_chkbox").find("input").click(function() { drawchart(); });


// tooltip function start
// tooltip function start
Line 200: Line 178:


     var previousPoint = null;
     var previousPoint = null;
     $("#placeholder").bind("plothover", function (event, pos, item) {
     $("#gene_exptable_chart").bind("plothover", function (event, pos, item) {
         $("#x").text(pos.x.toFixed(2));
         $("#x").text(pos.x.toFixed(2));
         $("#y").text(pos.y.toFixed(2));
         $("#y").text(pos.y.toFixed(2));
Line 208: Line 186:
                      
                      
                     $("#tooltip").remove();
                     $("#tooltip").remove();
//var gtest1 = oTable._('tr:eq('+ item.dataIndex +')', {"filter": "applied"})[0][0];
                    x = item.datapoint[0].toFixed(0),
                    y = item.datapoint[1].toFixed(2);


                    var x = item.datapoint[0].toFixed(0),
                        y = item.datapoint[1].toFixed(2);
                 
                     showTooltip(item.pageX, item.pageY,
                     showTooltip(item.pageX, item.pageY,
                               "Gene: "+ item.series.label +"<br>TPM: "+y);
                               "Sample: "+slist[item.dataIndex]+"<br>TSS: "+ item.series.label +" TPM: "+y);
//                              "Gene: "+ item.series.label +"<br>Sample: "+ gtest1 +"<br>TPM: "+y);
//test
//$("#test").css("background-color", item.series.color);
                 }
                 }
             }
             }
Line 228: Line 201:


// clicking point function
// clicking point function
     $("#placeholder").bind("plotclick", function (event, pos, item) {
     $("#gene_exptable_chart").bind("plotclick", function (event, pos, item) {
if (item){
if (item){
var vdata = Math.round($('#dynamic').height())/item.series.data.length*item.dataIndex;
var vdata = Math.round($('#gene_exptable').height())/item.series.data.length*item.dataIndex;
//var vdata = 600;
$('#gene_exptable_wrapper .dataTables_scrollBody').animate({ scrollTop: vdata-150 }, 'slow');
$('#dynamic_wrapper .dataTables_scrollBody').animate({ scrollTop: vdata-150 }, 'slow');
$("#gene_exptable_wrapper .dataTables_scrollBody tbody td").removeClass('highlight');
 
$('#gene_exptable_wrapper .dataTables_scrollBody tbody tr:eq(' + item.dataIndex+ ') td').addClass('highlight');
$("#dynamic_wrapper .dataTables_scrollBody tbody td").removeClass('highlight');
$('#dynamic_wrapper .dataTables_scrollBody tbody tr:eq(' + item.dataIndex+ ') td').addClass('highlight');
}
}
     });
     });
// clicking point function end
// clicking point function end


} );
} );
</script>
</script>
<span id="export_tool"></span><br><br>
</html>
</html>


<span id="export_tool"></span>
<includeonly>{{#gene_exptable:{{#switch:{{{tax_id}}}|9606=Hg19|10090=Mm9}}
<table class="entrezene_explist" id="dynamic"><html><thead></html>
|{{#ask:[[Category:FFCP]][[Short description::p1@{{{Symbol}}}]]|mainlabel=-|?phase1_expression|link=none|format=list|headers=hide|limit=1|intro=p1@{{{Symbol}}},|searchlabel=}}|{{#ask:[[Category:FFCP]][[Short description::p2@{{{Symbol}}}]]|mainlabel=-|?phase1_expression|link=none|format=list|headers=hide|limit=1|intro=p2@{{{Symbol}}},|searchlabel=}}|{{#ask:[[Category:FFCP]][[Short description::p3@{{{Symbol}}}]]|mainlabel=-|?phase1_expression|link=none|format=list|headers=hide|limit=1|intro=p3@{{{Symbol}}},|searchlabel=}}|{{#ask:[[Category:FFCP]][[Short description::p4@{{{Symbol}}}]]|mainlabel=-|?phase1_expression|link=none|format=list|headers=hide|limit=1|intro=p4@{{{Symbol}}},|searchlabel=}}|{{#ask:[[Category:FFCP]][[Short description::p5@{{{Symbol}}}]]|mainlabel=-|?phase1_expression|link=none|format=list|headers=hide|limit=1|intro=p5@{{{Symbol}}},|searchlabel=}}
<tr>
}}</includeonly>
<th>sample</th>
<th><div  class="rotate90"><p>
{{#ask:[[Category:FFCP]][[EntrezGene::{{{GeneID}}}]]|?id|?short_description|limit=100|format=template|template=Entrezgene_cpphase1_exptable_header_{{#switch:{{{tax_id}}}|9606=hg19|10090=mm9}}|sep=</p></div></th><th><div  class="rotate90"><p>}}
</p></div></th>
</tr><html></thead><tbody></html>
{{#exptable_{{#switch:{{{tax_id}}}|9606=hg19|10090=mm9}}:
{{#ask:[[Category:FFCP]][[EntrezGene::{{{GeneID}}}]]
|?Phase1 expression
|limit=100
|format=list
|headers=hide
|sep=;;
|template=Ask1stprop
}}
}}
<html></tbody></html></table>
 
<br><br>
<br><br>
<html>
<div id="gene_exptable_chart" style="float:left;width:600px;height:300px;"></div>
<div id="placeholder" style="float:left;width:600px;height:300px;"></div>
<html><br><br></html>
<div id="chart_chkbox" style="float:left;"></div>
<div id="gene_exptable_chart_chkbox" style="float:left;"></div>
<div style="clear:both;"></div>
<div style="clear:both;"></div>


</html>
}}
== Details ==
<table>
<tr><th scope="row" align="right">GeneID:</th><td>[[GeneID::{{{GeneID}}}]]</td></tr>
<tr><th scope="row" align="right">LocusTag:</th><td>[[LocusTag::{{{LocusTag}}}]]</td></tr>
<tr><th scope="row" align="right">chromosome:</th><td>[[chromosome::{{{chromosome}}}]]</td></tr>
<tr><th scope="row" align="right">map location:</th><td>{{#show:{{FULLPAGENAME}}|?map_location}}</td></tr>
<tr><th scope="row" align="right">type of gene:</th><td>[[type_of_gene::{{{type_of_gene}}}]]</td></tr>
<tr><th scope="row" align="right">Symbol from <br>nomenclature authority:</th><td>[[Symbol_from_nomenclature_authority::{{{Symbol_from_nomenclature_authority}}}]]</td></tr>
<tr><th scope="row" align="right">Full name from <br> nomenclature authority:</th><td>[[Full_name_from_nomenclature_authority::{{{Full_name_from_nomenclature_authority}}}]]</td></tr>
<tr><th scope="row" align="right">Nomenclature status:</th><td>[[Nomenclature_status::{{{Nomenclature_status}}}]]</td></tr>
<tr><th scope="row" align="right">Other designations:</th><td>{{#show:{{FULLPAGENAME}}|?Other_designations}}</td></tr>
<tr><th scope="row" align="right">Modification date:</th><td>[[Modification_date::{{{Modification_date}}}]]</td></tr>
<tr><th scope="row" align="right">transcription factor:</th><td>[[transcription_factor::{{{transcription_factor}}}]]</td></tr>
</table>


*Click each plot point to find sample in table
<html><style type="text/css"> 
table.details td { width:35%; background-color: #EAEBFF;}
table.details th { width:15%; background-color: #5A5FB5; color: white;}
</style></html>


== ENCODE TF ChIP-seq peak enrichment analysis ==
{{Fontsize|3|ENCODE TF ChIP-seq peak enrichment analysis }}{{#info:Analyst: Erik Arner <br>Summary: For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <nowiki><=</nowiki>  0.05)  after Benjamini-Hochberg correction were retained.  <br>
{{#info: Method: For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <nowiki><=</nowiki>  0.05)  after Benjamini-Hochberg correction were retained.  <br>Analyst: Erick Arner}}  
<br><br>link to source dataset.<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters data]
}}  
----
{{#ifexpr: {{#ask:[[tf_chipseq_enrich_entregeneid::{{{GeneID}}}]]|format=count}} > 0 |
{{#ifexpr: {{#ask:[[tf_chipseq_enrich_entregeneid::{{{GeneID}}}]]|format=count}} > 0 |
(#promoters = Number of promoters in cluster that have ChIP signal of the TF)  
(#promoters = Number of promoters in the coexpression cluster that have ChIP signal of the TF)  
<html>
<html>
<script type="text/javascript">
<script type="text/javascript">
$(document).ready(function() {
$(document).ready(function() {
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</html>{{#ask:[[tf_chipseq_enrich_entregeneid::{{{GeneID}}}]]|?Tf_chipseq_enrich_values|intro=<div style="width:100%; float:left;"><table id="tf_chipseq_enrich" class="stripe cell-border order-column compact"><html><thead></html><tr><th>Coexpression cluster</th><th>#promoters</th><th>Enrichment</th><th>p-value</th><th>q-value</th></tr><html></thead><tbody></html>|outro=<html></tbody></html></table></div>|link=none|format=template|template=Tf_chipseq_enrichlist_in_entregene|limit=5000|searchlabel=}}
{{#ask:[[tf_chipseq_enrich_entregeneid::{{{GeneID}}}]]|?Tf_chipseq_enrich_values|intro=<table id="tf_chipseq_enrich"><html><thead></html><tr><th>Coexpression cluster</th><th>#promoters</th><th>Enrichment</th><th>p-value</th><th>q-value</th></tr><html></thead><tbody></html>|outro=<html></tbody></html></table>|link=none|format=template|template=Tf_chipseq_enrichlist_in_entregene|searchlabel=}}
|No analysis results for this cluster
|No analysis results for this cluster
}}
}}
<html><br><br></html>
{{Fontsize|3|Details}}{{#info:<b>Summary:</b>It includes sequences from the international sequence collaboration, Swiss-Prot, and RefSeq. The RefSeq subset of this file is also available as gene2refseq.<br><br>links to source dataset.<br>[ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz  human] <br>
[ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Mus_musculus.gene_info.gz  mouse]
}}
----
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<tr><th scope="row" align="right">GeneID:</th><td>{{#if:{{{GeneID}}}|[[GeneID::{{{GeneID}}}]]|NA}}</td></tr>
<tr><th scope="row" align="right">LocusTag:</th><td>{{#if:{{{LocusTag}}}|[[LocusTag::{{{LocusTag}}}]]|NA}}</td></tr>
<tr><th scope="row" align="right">chromosome:</th><td>{{#if:{{{chromosome}}}|[[chromosome::{{{chromosome}}}]]|NA}}</td></tr>
<tr><th scope="row" align="right">map location:</th><td>{{#show:{{FULLPAGENAME}}|?map_location}}</td></tr>
<tr><th scope="row" align="right">type of gene:</th><td>{{#if:{{{type_of_gene}}}|[[type_of_gene::{{{type_of_gene}}}]]|NA}}</td></tr>
<tr><th scope="row" align="right">Symbol from <br>nomenclature authority:</th><td>{{#if:{{{Symbol_from_nomenclature_authority}}}|[[Symbol_from_nomenclature_authority::{{{Symbol_from_nomenclature_authority}}}]]|NA}}</td></tr>
<tr><th scope="row" align="right">Full name from <br> nomenclature authority:</th><td>{{#if:{{{Full_name_from_nomenclature_authority}}}|[[Full_name_from_nomenclature_authority::{{{Full_name_from_nomenclature_authority}}}]]|NA}}</td></tr>
<tr><th scope="row" align="right">Nomenclature status:</th><td>{{#if:{{{Nomenclature_status}}}|[[Nomenclature_status::{{{Nomenclature_status}}}]]|NA}}</td></tr>
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<tr><th scope="row" align="right">Modification date:</th><td>{{#if:{{{Modification_date}}}|{{#time: d.m.Y |{{{Modification_date}}}}}|NA}}</td></tr>
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Line 316: Line 286:
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{{#arraymap:{{{map_location}}}|;;|$|{{#set:map_location=$}}}}
{{#arraymap:{{{Other_designations}}}|;;|$|{{#set:Other_designations=$}}}}
{{#arraymap:{{{Other_designations}}}|;;|$|{{#set:Other_designations=$}}}}


[[Category:EntrezGene]]
[[Category:EntrezGene]]
<html>
 
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{{#set:GeneID={{{GeneID}}}}}
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{{#set:chromosome={{{chromosome}}}}}
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<span><br><br>
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Revision as of 15:01, 14 November 2019

Symbol:{{{Symbol}}}
Description:{{{description}}}
Synonyms:
Species:NA
Xrefs:
EntrezGene:{{{GeneID}}}
{{{dbXrefs}}}:[NA ]
Associated motifs:NA
Transcripton Factor?: No

TSS regions




View on UCSC genome browser


Mouse over to see Genome browser image, Click image to go to Genome browser


TSS expression










  • Click each plot point to find sample in table

ENCODE TF ChIP-seq peak enrichment analysis Analyst: Erik Arner <br>Summary: For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><br><br>link to source dataset.<br>data


No analysis results for this cluster

Details<b>Summary:</b>It includes sequences from the international sequence collaboration, Swiss-Prot, and RefSeq. The RefSeq subset of this file is also available as gene2refseq.<br><br>links to source dataset.<br>human <br>mouse


GeneID:{{{GeneID}}}
LocusTag:{{{LocusTag}}}
chromosome:{{{chromosome}}}
map location:
type of gene:{{{type_of_gene}}}
Symbol from
nomenclature authority:
{{{Symbol_from_nomenclature_authority}}}
Full name from
nomenclature authority:
{{{Full_name_from_nomenclature_authority}}}
Nomenclature status:{{{Nomenclature_status}}}
Other designations:
Modification date:Error: Invalid time.