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{{Loading|loadingimage=sprites.gif}}<html><style type="text/css">
+
{{Loading|loadingimage=sprites.gif}}<html><script type="text/javascript" src="/5/sstar/jquery-1.7.1.min.js"></script>
table.detailinfo td { background-color: #FFFFFF;}
+
<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>
table.detailinfo th { background-color: #fbfffb; color:#054950;}
+
<script type="text/javascript" src="/5/sstar/rb_js/custom/convert.js"></script></html>
</style></html>
+
<table>
<div style="width:100%; float:none;">
+
<tr><th scope="row" align="right" valign="top">[[Property:Symbol|Symbol]]:</th><td>{{#if:{{{Symbol}}}|[[Symbol::{{{Symbol}}}]]|NA}}</td></tr>
<table class="detailinfo">
+
<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:Symbol|Symbol]]:</th><td>{{#if:{{{Symbol}}}|[[Symbol::{{{Symbol}}}]]|NA}}</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"> [[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>{{#if:{{{Synonyms}}}|{{#show:{{FULLPAGENAME}}|?Synonyms}}|NA}}</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">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">External refs:</th><td>{{#if:{{{GeneID}}}|''EntrezGene'':[http://www.ncbi.nlm.nih.gov/gene/{{{GeneID}}} {{{GeneID}}}]{{#arraydefine:gene_raw_array|{{{dbXrefs}}}|;;}}{{#vardefine:species_temp|{{#switch:{{{tax_id}}}|9606=Homo_sapiens|10090=Mus_musculus|NA}}}}{{#loop: i
+
<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>
  | 0         
+
--><tr><th scope="row" align="right" valign="top">Xrefs:</th><td>{{#if:{{{GeneID}}}|{{GeneExternalRefs|{{{tax_id}}}|{{{chromosome}}}|{{{GeneID}}}|{{{Symbol}}}|{{{Synonyms}}}|{{{dbXrefs}}}}}|NA}}</td></tr>
  | {{#arraysize:gene_raw_array}}
+
<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}}|}}
  | <nowiki/>{{#arraydefine:elements|{{#arrayindex:gene_raw_array|{{#var:i}} }}|:|}}{{#vardefine:RESOURCE_URL_BUILD|{{#switch:{{#arrayindex:elements |0}}|HGNC=http://www.genenames.org/data/hgnc_data.php?hgnc_id={{#arrayindex:elements |1}}|MIM=http://www.omim.org/entry/{{#arrayindex:elements |1}}|Ensembl=http://asia.ensembl.org/{{#var:species_temp}}/Gene/Summary?db=core;g={{#arrayindex:elements |1}}|HPRD=http://www.hprd.org/summary?hprd_id={{#arrayindex:elements |1}}&isoform_id={{#arrayindex:elements |1}}_1&isoform_name=Isoform_1|Vega=http://vega.sanger.ac.uk/{{#var:species_temp}}/Gene/Summary?db=core;g={{#arrayindex:elements |1}}|MGI=http://www.informatics.jax.org/marker/MGI:{{#arrayindex:elements |1}}|NA}}}}''{{#arrayindex:elements |0}}'':[{{#var:RESOURCE_URL_BUILD}} {{#arrayindex:elements |1}}]
 
|NA}}}}
 
</td></tr>
 
<!--tr><th scope="row" align="right" valign="top">External refs:</th><td>{{#if:{{{GeneID}}}|{{GeneExternalRefs|{{{tax_id}}}|{{{chromosome}}}|{{{GeneID}}}|{{{Symbol}}}|{{{Synonyms}}}|{{{dbXrefs}}}}}|NA}}</td></tr-->
 
<tr><th scope="row" align="right" valign="top">Associated motifs:</th><td>{{#ifeq:{{#expr:{{#ask:[[Category:SwissregulonMotif]][[EntrezGene::~{{{GeneID}}}]]|?name|format=count}}+{{#ask:[[Category:Motif]][[Name::~{{{Symbol}}}]]|?#|format=count}}+{{#ask:[[Category:NonRedundantMotifCluster]][[EntrezGene::~{{{GeneID}}}]]|?#|format=count}} }} | 0 | NA | {{#if:{{#ask:[[Category:SwissregulonMotif]][[EntrezGene::~{{{GeneID}}}]]}}|{{#ask:[[Category:SwissregulonMotif]][[EntrezGene::~{{{GeneID}}}]]
 
|?name
 
|format=template
 
|link=none
 
|template=SwissregulonResult_withSeqLogo
 
|sep=
 
}}|
 
}}
 
<span><br><br>
 
{{#if:{{#ask:[[Category:Motif]][[Name::~{{{Symbol}}}]]}}| {{#ask:[[Category:Motif]][[Name::~{{{Symbol}}}]]|template=Jasparlogo_genepage|link=none}}|}}
 
</span>
 
 
<span>{{#arraymap:{{{GeneID}}}|,|$|
 
<span>{{#arraymap:{{{GeneID}}}|,|$|
 
{{NonRedundantMotifRender|$}}  
 
{{NonRedundantMotifRender|$}}  
Line 33: Line 16:
 
</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>
 
<tr><th scope="row" align="right" valign="top">Transcripton Factor?: </th><td>{{#switch:{{{tf?}}}|yes=[[tf?::Yes]]|[[tf?::No]]}}</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
 
|sort=Short description
 
}}
 
</td></tr>
 
 
</table>
 
</table>
</div>
+
 
 +
{{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 53: Line 40:
 
});
 
});
 
</script>
 
</script>
</html>
+
</html><br>
<h2>View on UCSC genome browser OSC local mirror</h2>
+
{{Fontsize|3|View on UCSC genome browser }}
 +
----
 
<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}}}]]|link=none|headers=hide|limit=1|searchlabel=}}|FFCP_PHASE1:|}}|https://fantom5-collaboration.gsc.riken.jp/ucsc/|3000}}
+
{{#ucsc_gb_link:{{#replace:{{#ask:[[Category:FFCP]][[Short description::p1@{{{Symbol}}}]][[FFCP PHASE1:+]]|link=none|headers=hide|limit=1|searchlabel=}}|FFCP PHASE1:|}}}}
</div>
+
</div><br>
 
+
{{Fontsize|3|TSS expression}}
== TSS expression ==
+
----
 
<html>
 
<html>
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.min.js"></script>
+
<script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.min.js"></script>
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script>
+
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script>
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/flot/jquery.flot.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">
 
<style type="text/css" title="currentStyle">
@import "/resource_browser/rb_js/datatables/media/css/jquery.dataTables.css";
+
@import "/5/sstar/rb_js/html5button/datatables.css";
@import "/resource_browser/rb_js/datatables/extras/TableTools/media/css/TableTools.css";
+
@import "/5/sstar/rb_js/datatables/extras/TableTools/media/css/TableTools.css";
 
</style>
 
</style>
  
 
</html>
 
</html>
 +
 
<html>
 
<html>
 
<style type="text/css">   
 
<style type="text/css">   
Line 84: Line 73:
 
<script type="text/javascript">
 
<script type="text/javascript">
 
$(document).ready(function() {
 
$(document).ready(function() {
     var oTable =  $('#gene_exptable').dataTable({
+
     var oTable =  $('#gene_exptable').DataTable({
"sScrollY": "300px",
+
                dom: 'Bfrti',
"bPaginate": false,
+
scrollY: "300px",
"bScrollCollapse": true,
+
scrollCollapse: true,
"iDisplayLength": -1,
+
                paging: false,
"aaSorting": [[1,'desc']],
+
order: [[1,'desc']],
"aoColumnDefs": [{ "asSorting": [ "asc", "desc" ], "sType": "html", "aTargets": [ 0 ] }, { "asSorting": [ "desc", "asc" ], "aTargets": [ "_all" ] } ]
+
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");
 
$('#gene_exptable_wrapper .dataTables_scrollHead th').css("height", "100px").css("vertical-align", "bottom");
Line 97: Line 87:
 
var data = [];
 
var data = [];
 
var plotdata = [];
 
var plotdata = [];
 
+
var slist = [];
 
 
 
// chart checkbox
 
// chart checkbox
for (var i2=1; i2<oTable.fnSettings().aoColumns.length; i2++){
+
for (var i2=1; i2<$('#gene_exptable thead th').length; i2++){
 
key2 = i2-1;
 
key2 = i2-1;
 
         $("#gene_exptable_chart_chkbox").append('<input type="checkbox" name="' + key2 +
 
         $("#gene_exptable_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 + '">'
                                 + $(oTable.fnSettings().aoColumns[i2].sTitle).text() + '</label><br/>');
+
                                 + $('#gene_exptable thead th:nth-child('+(i2+1)+')').text() + '</label><br/>');
 
}
 
}
 
+
$(oTable.settings().column(i2).title).text()
 
function collectdata(){
 
function collectdata(){
 
data = [];
 
data = [];
for (i2=1, len2=oTable.fnSettings().aoColumns.length; i2<len2; i2++){
+
// for (i2=1, len2=oTable.settings().columns.length; i2<len2; i2++){
 +
for (i2=1, len2=$('#gene_exptable thead th').length; i2<len2; i2++){
 +
 
 
var plots = [];
 
var plots = [];
 
for (i1=2, len1=$('#gene_exptable tr').length; i1<len1; i1++) {
 
for (i1=2, len1=$('#gene_exptable tr').length; i1<len1; i1++) {
 
     plots.push([i1,$("#gene_exptable tr")[i1].cells[i2].innerHTML]);
 
     plots.push([i1,$("#gene_exptable tr")[i1].cells[i2].innerHTML]);
 
}
 
}
data.push({"label": $(oTable.fnSettings().aoColumns[i2].sTitle).text(), "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 188: Line 183:
 
                     x = item.datapoint[0].toFixed(0),
 
                     x = item.datapoint[0].toFixed(0),
 
                     y = item.datapoint[1].toFixed(2);
 
                     y = item.datapoint[1].toFixed(2);
                 
+
 
 
                     showTooltip(item.pageX, item.pageY,
 
                     showTooltip(item.pageX, item.pageY,
                               "TSS: "+ item.series.label +"<br>TPM: "+y);
+
                               "Sample: "+slist[item.dataIndex]+"<br>TSS: "+ item.series.label +" TPM: "+y);
 
                 }
 
                 }
 
             }
 
             }
Line 210: Line 205:
 
     });
 
     });
 
// clicking point function end
 
// clicking point function end
 
var oTableTools = new TableTools(oTable, {"sSwfPath": "/5/sstar/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 );
 
 
  
  
 
} );
 
} );
 
</script>
 
</script>
<span id="export_tool"></span>
+
<span id="export_tool"></span><br><br>
 
</html>
 
</html>
  
{{#gene_exptable:{{#switch:{{{tax_id}}}|9606=Hg19|10090=Mm9}}
+
<includeonly>{{#gene_exptable:{{#switch:{{{tax_id}}}|9606=Hg19|10090=Mm9}}
 
|{{#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=}}
 
|{{#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=}}
}}
+
}}</includeonly>
 
<br><br>
 
<br><br>
 
<div id="gene_exptable_chart" style="float:left;width:600px;height:300px;"></div>
 
<div id="gene_exptable_chart" style="float:left;width:600px;height:300px;"></div>
<br>
+
<html><br><br></html>
 
<div id="gene_exptable_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>
Line 238: Line 228:
 
</style></html>
 
</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 the coexpression cluster that have ChIP signal of the TF)  
 
(#promoters = Number of promoters in the coexpression cluster that have ChIP signal of the TF)  
Line 245: Line 237:
 
<script type="text/javascript">
 
<script type="text/javascript">
 
$(document).ready(function() {
 
$(document).ready(function() {
     var oTable2= $('#tf_chipseq_enrich').dataTable({
+
     var oTable2 = $('#tf_chipseq_enrich').DataTable({
"sScrollY": "300px",
+
        dom: 'Blfrtip',
"bPaginate": false,
+
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
"bScrollCollapse": true,
+
scrollY: "300px",
"iDisplayLength": -1,
+
scrollCollapse: true,
"aaSorting": [[4,'asc']],
+
        pageLength: 10,
"aoColumnDefs": [{ "sWidth": "150px", "sType": "numeric", "aTargets": [3] },{ "sWidth": "150px", "sType": "numeric", "aTargets": [4] }]
+
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
});
+
order: [[4,'asc']],
var oTableTools2 = new TableTools( oTable2, {"sSwfPath": "/5/sstar/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"} ]});
+
columnDefs: [{type: "numeric", targets: [2,3,4],
 
+
        render: function ( data, type, row, meta ) {
$('#export_tool2').before( oTableTools2.dom.container );
+
                  var num =data;             
 +
                  return exp_converter(num,2,"e") ;
 +
} }]
 +
});
 
});
 
});
 
</script>
 
</script>
<span id="export_tool2"></span>
+
</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=}}
</html>{{#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|limit=5000|searchlabel=}}
 
 
|No analysis results for this cluster
 
|No analysis results for this cluster
 
}}
 
}}
 
<html><br><br></html>
 
<html><br><br></html>
== 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>data source :<br>[https://fantom5-collaboration.gsc.riken.jp/files/data/shared/external/entrez_gene/2012-01-19/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz  human]
+
{{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>
<br>[https://fantom5-collaboration.gsc.riken.jp/files/data/shared/external/entrez_gene/2012-01-19/DATA/GENE_INFO/Mammalia/Mus_musculus.gene_info.gz  mouse]
+
[ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Mus_musculus.gene_info.gz  mouse]
 
}}
 
}}
 +
----
 
<table class="details">
 
<table class="details">
 
<tr><th scope="row" align="right">GeneID:</th><td>{{#if:{{{GeneID}}}|[[GeneID::{{{GeneID}}}]]|NA}}</td></tr>
 
<tr><th scope="row" align="right">GeneID:</th><td>{{#if:{{{GeneID}}}|[[GeneID::{{{GeneID}}}]]|NA}}</td></tr>
Line 277: Line 272:
 
<tr><th scope="row" align="right">Nomenclature status:</th><td>{{#if:{{{Nomenclature_status}}}|[[Nomenclature_status::{{{Nomenclature_status}}}]]|NA}}</td></tr>
 
<tr><th scope="row" align="right">Nomenclature status:</th><td>{{#if:{{{Nomenclature_status}}}|[[Nomenclature_status::{{{Nomenclature_status}}}]]|NA}}</td></tr>
 
<tr><th scope="row" align="right">Other designations:</th><td>{{#if:{{{Other_designations}}}|{{#show:{{FULLPAGENAME}}|?Other_designations}}|NA}}</td></tr>
 
<tr><th scope="row" align="right">Other designations:</th><td>{{#if:{{{Other_designations}}}|{{#show:{{FULLPAGENAME}}|?Other_designations}}|NA}}</td></tr>
<tr><th scope="row" align="right">Modification date:</th><td>{{#if:{{{Modification_date}}}|[[Modification_date::{{{Modification_date}}}]]|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>
 
</table>
 
</table>
 
 
 
  
  
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[[Category:EntrezGene]]
 
[[Category:EntrezGene]]
<html>
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<script language="javascript" type="text/javascript" src="/resource_browser/rb_js/flot/jquery.flot.js"></script>
+
{{#set:GeneID={{{GeneID}}}}}
<script language="javascript" type="text/javascript" src="/resource_browser/rb_js/flot/jquery.flot.axislabels.js"></script>
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{{#set:LocusTag ={{{LocusTag}}}}}
</html>
+
{{#set:chromosome={{{chromosome}}}}}
 +
{{#set:type_of_gene={{{type_of_gene}}}}}
 +
{{#set:map_location={{{map_location}}}}}
 +
{{#set:Symbol_from_nomenclature_authority={{{Symbol_from_nomenclature_authority}}}}}
 +
{{#set:Full_name_from_nomenclature_authority={{{Full_name_from_nomenclature_authority}}}}}
 +
{{#set:Nomenclature_status={{{Nomenclature_status}}}}}
 +
{{#set:Other_designations={{{Other_designations}}}}}
 +
<!--
 +
{{#set:Modification_date={{{Modification_date}}}}}
 +
-->
 +
 
 +
<!--{{#ask:[[Category:SwissregulonMotif]][[EntrezGene::~{{{GeneID}}}]]|?name|format=count}}{{#if:{{#ask:[[Category:SwissregulonMotif]][[EntrezGene::~{{{GeneID}}}]]}}|{{#ask:[[Category:SwissregulonMotif]][[EntrezGene::~{{{GeneID}}}]]
 +
|?name
 +
|format=template
 +
|link=none
 +
|template=SwissregulonResult_withSeqLogo
 +
|sep=
 +
}}|
 +
}}
 +
<span><br><br>
 +
-->

Latest revision as of 08:24, 21 June 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
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.


link to source dataset.
data


No analysis results for this cluster

DetailsSummary:It includes sequences from the international sequence collaboration, Swiss-Prot, and RefSeq. The RefSeq subset of this file is also available as gene2refseq.

links to source dataset.
human
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.