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Difference between revisions of "Template:EntrezGene"

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Line 19: Line 19:
 
{{Fontsize|3|TSS regions }}
 
{{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}}
+
<span id="ffcp_list_table_export_tool"></span>
 +
{{#ask:[[FFCP PHASE2:+]][[Category:FFCP]][[EntrezGene::{{{GeneID}}}]]|?Short_description|format=ttable|mainlabel=TSS peak ID|class=ffcp_list|limit=20000}}
 
<br>
 
<br>
 
<html>
 
<html>
Line 25: Line 26:
 
$(document).ready(function() {  
 
$(document).ready(function() {  
 
// TSS regions list
 
// TSS regions list
$('.ffcp_list').DataTable({
+
  var ffcp_list_table = $('.ffcp_list').dataTable();
        dom: 'Blfrtip',
+
  var  ffcp_list_table_tools = new TableTools( ffcp_list_table, {"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"} ]});
        lengthMenu: [[10, 25, 50, -1], [10, 25, 50, "All"]],
+
 
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5']
+
$('#ffcp_list_table_export_tool').before(ffcp_list_table_tools.dom.container );
});
 
  
 
// hide-show animation for ucsc genome browser view
 
// hide-show animation for ucsc genome browser view
Line 49: Line 49:
 
----
 
----
 
<html>
 
<html>
<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/media/js/jquery.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="/resource_browser/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="/resource_browser/rb_js/flot/jquery.flot.min.js"></script>
 
<style type="text/css" title="currentStyle">
 
<style type="text/css" title="currentStyle">
@import "/5/sstar/rb_js/html5button/datatables.css";
+
@import "/resource_browser/rb_js/datatables/media/css/jquery.dataTables.css";
 
@import "/resource_browser/rb_js/datatables/extras/TableTools/media/css/TableTools.css";
 
@import "/resource_browser/rb_js/datatables/extras/TableTools/media/css/TableTools.css";
 
</style>
 
</style>
Line 72: Line 72:
 
<script type="text/javascript">
 
<script type="text/javascript">
 
$(document).ready(function() {
 
$(document).ready(function() {
     var oTable =  $('#gene_exptable').DataTable({
+
     var oTable =  $('#gene_exptable').dataTable({
        dom: 'Blfrti',
+
"sScrollY": "300px",
scrollY: "300px",
+
"bPaginate": false,
scrollCollapse: true,
+
"bScrollCollapse": true,
pageLength: "-1",
+
"iDisplayLength": -1,
order: [[1,'desc']],
+
"aaSorting": [[1,'desc']],
buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
+
"aoColumnDefs": [{ "asSorting": [ "asc", "desc" ], "sType": "html", "aTargets": [ 0 ] }, { "asSorting": [ "desc", "asc" ], "aTargets": [ "_all" ] } ]
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 87: Line 86:
 
var plotdata = [];
 
var plotdata = [];
 
var slist = [];
 
var slist = [];
 +
 
// chart checkbox
 
// chart checkbox
for (var i2=1; i2<$('#gene_exptable thead th').length; i2++){
+
for (var i2=1; i2<oTable.fnSettings().aoColumns.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 + '">'
                                 + $('#gene_exptable thead th:nth-child('+(i2+1)+')').text() + '</label><br/>');
+
                                 + $(oTable.fnSettings().aoColumns[i2].sTitle).text() + '</label><br/>');
 
}
 
}
$(oTable.settings().column(i2).title).text()
+
 
 
function collectdata(){
 
function collectdata(){
 
data = [];
 
data = [];
// for (i2=1, len2=oTable.settings().columns.length; i2<len2; i2++){
+
for (i2=1, len2=oTable.fnSettings().aoColumns.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": $('#gene_exptable thead th:nth-child('+(i2+1)+')').text(), "data": plots});
+
data.push({"label": $(oTable.fnSettings().aoColumns[i2].sTitle).text(), "data": plots});
 
}
 
}
 
slist = [];
 
slist = [];
Line 205: Line 203:
 
// 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 236: Line 238:
 
<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({
        dom: 'Blfrtip',
+
"sScrollY": "300px",
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
+
"bScrollCollapse": true,
scrollY: "300px",
+
"bPaginate": true,
scrollCollapse: true,
+
"bFilter": true,
        pageLength: 10,
+
"bInfo": true,
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
+
                "iDisplayLength": 10,
order: [[4,'asc']],
+
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
columnDefs: [{type: "numeric", targets: [2,3,4],
+
"aaSorting": [[4,'asc']],
        render: function ( data, type, row, meta ) {
+
"aoColumnDefs": [{"sType": "numeric", "aTargets": [2,3,4],"fnRender": function (obj) {                  
                   var num =data;               
+
                   var num =obj.aData[obj.iDataColumn];               
 
                   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>
</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=}}
+
<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"><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
 
}}
 
}}

Revision as of 01:29, 8 March 2018

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.