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Difference between revisions of "Template:EntrezGene"

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Line 1: Line 1:
{{Loading|loadingimage=sprites.gif}}<html><script language="javascript" type="text/javascript" src="/resource_browser/rb_js/flot/jquery.flot.js"></script><script language="javascript" type="text/javascript" src="/resource_browser/rb_js/flot/jquery.flot.axislabels.js"></script>
+
{{Loading|loadingimage=sprites.gif}}<html><script type="text/javascript" src="/5/sstar/jquery-1.7.1.min.js"></script>
<script type="text/javascript" src="/resource_browser/rb_js/custom/convert.js"></script></html>
+
<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>{{#if:{{{Symbol}}}|[[Symbol::{{{Symbol}}}]]|NA}}</td></tr>
 
<tr><th scope="row" align="right" valign="top">[[Property:Symbol|Symbol]]:</th><td>{{#if:{{{Symbol}}}|[[Symbol::{{{Symbol}}}]]|NA}}</td></tr>
Line 9: Line 10:
 
<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">[[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">Xrefs:</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}}}]]
+
<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}}|}}
|?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 25: 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>{{#if:{{#ask:[[Category:FFCP]][[EntrezGene::{{{GeneID}}}]]
 
|?Short description
 
|format=ul
 
|headers=hide
 
|sort=Short description
 
}}|{{#ask:[[Category:FFCP]][[EntrezGene::{{{GeneID}}}]]
 
|?Short description
 
|format=ul
 
|headers=hide
 
|sort=Short description
 
}}|NA}}
 
</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 49: Line 40:
 
});
 
});
 
</script>
 
</script>
</html>
+
</html><br>
{{Fontsize|3|View on UCSC genome browser OSC local mirror}}
+
{{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><br>
 
</div><br>
 
{{Fontsize|3|TSS expression}}
 
{{Fontsize|3|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>
  
Line 82: 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 96: Line 88:
 
var plotdata = [];
 
var plotdata = [];
 
var slist = [];
 
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 = [];
 
slist = [];
Line 213: Line 206:
 
// clicking point function end
 
// clicking point function end
  
 
 
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 );
 
  
 
} );
 
} );
Line 223: Line 212:
 
</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>
Line 248: 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',
"bScrollCollapse": true,
+
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
"bPaginate": true,
+
scrollY: "300px",
"bFilter": true,
+
scrollCollapse: true,
"bInfo": true,
+
        pageLength: 10,
                "iDisplayLength": 10,
+
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
+
order: [[4,'asc']],
"aaSorting": [[4,'asc']],
+
columnDefs: [{type: "numeric", targets: [2,3,4],
"aoColumnDefs": [{"sType": "numeric", "aTargets": [2,3,4],"fnRender": function (obj) {                  
+
        render: function ( data, type, row, meta ) {
                   var num =obj.aData[obj.iDataColumn];               
+
                   var num =data;               
 
                   return exp_converter(num,2,"e") ;
 
                   return exp_converter(num,2,"e") ;
} }]
+
} }]
});
+
});
var oTableTools2 = new TableTools(oTable2, {"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_tool2').before( oTableTools2.dom.container );
 
 
});
 
});
 
</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=<div style="width:100%; float:left;"><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></div>|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
 
}}
 
}}
Line 299: Line 284:
  
 
[[Category:EntrezGene]]
 
[[Category:EntrezGene]]
 +
 +
{{#set:GeneID={{{GeneID}}}}}
 +
{{#set:LocusTag ={{{LocusTag}}}}}
 +
{{#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>
 +
-->

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.