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Difference between revisions of "Template:Coexpression clusters"

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Line 1: Line 1:
 
{{Loading|loadingimage=sprites.gif}}<html>
 
{{Loading|loadingimage=sprites.gif}}<html>
<script type="text/javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.min.js"></script>
+
<script type="text/javascript" src="/5/sstar/jquery-1.7.1.min.js"></script>
<script type="text/javascript" src="/resource_browser/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script>
+
<script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.min.js"></script>
<script type="text/javascript" src="/resource_browser/rb_js/custom/convert.js"></script>
+
<script type="text/javascript" src="/5/sstar/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script>
 +
<script type="text/javascript" src="/5/sstar/rb_js/custom/convert.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";
  
 
.table_title{
 
.table_title{
Line 17: Line 18:
 
$(document).ready(function() {
 
$(document).ready(function() {
 
// FFCP list start
 
// FFCP list start
var ffcp_list_table = $('.ffcp_list').dataTable();
+
var ffcp_list_table = $('.ffcp_list').DataTable({
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"} ]});
+
    dom: 'Blfrtip',
 
+
    lengthMenu: [[10, 25, 50, -1], [10, 25, 50, "All"]],
$('#ffcp_list_table_export_tool').before(ffcp_list_table_tools.dom.container );
+
    buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
 +
    columns: [{title:"Id"},{title:"Short description"}]
 +
});
 
// FFCP list end
 
// FFCP list end
var pathway_enrichment_flag="</html>{{{pathway_enrichment}}}<html>";
+
if($('.pathway_enrichment').size()>0) {
if(pathway_enrichment_flag.length>5){
 
 
// Pathway enrichment analysis start
 
// Pathway enrichment analysis start
var pathway_enrichment_table =$('.pathway_enrichment').dataTable({
+
var pathway_enrichment_table =$('.pathway_enrichment').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: [[1,'asc']],
"aaSorting": [[1,'asc']],
+
columnDefs: [{render: function ( data, type, row, meta ) {
"aoColumnDefs": [{"fnRender": function ( o, val ) {
+
var name = data.split(":");
var name = o.aData[4].split(":");
+
if(name[0].indexOf("KEGG")!=-1){
if(name[0].indexOf("KEGG") != -1){
 
 
return "<a href=\"http://www.genome.jp/dbget-bin/www_bget?pathway:map"+name[1]+"\">"+name[0]+"</a>";
 
return "<a href=\"http://www.genome.jp/dbget-bin/www_bget?pathway:map"+name[1]+"\">"+name[0]+"</a>";
}else if(name[0].indexOf("Wikipathways") != -1){
+
}else if(name[0].indexOf("Wikipathways")!=-1){
 
return "<a href=\"http://www.wikipathways.org/index.php/Pathway:"+name[1]+"\">"+name[0]+"</a>";
 
return "<a href=\"http://www.wikipathways.org/index.php/Pathway:"+name[1]+"\">"+name[0]+"</a>";
}else if(name[0].indexOf("Reactome") != -1){
+
}else if(name[0].indexOf("Reactome")!=-1){
 
return "<a href=\"http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID="+name[1]+"\">"+name[0]+"</a>";
 
return "<a href=\"http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID="+name[1]+"\">"+name[0]+"</a>";
}else if(name[0].indexOf("Netpath") != -1){
+
}else if(name[0].indexOf("Netpath")!=-1){
 
return "<a href=\"http://www.netpath.org/pathways?path_id="+name[1]+"\">"+name[0]+"</a>";
 
return "<a href=\"http://www.netpath.org/pathways?path_id="+name[1]+"\">"+name[0]+"</a>";
}else if(name[0].indexOf("Static Module") != -1){
+
}else if(name[0].indexOf("Static Module")!=-1){
 
return "<a href=\"http://genomebiology.com/content/11/5/R53\">"+name[0]+"</a>";
 
return "<a href=\"http://genomebiology.com/content/11/5/R53\">"+name[0]+"</a>";
 
}else{
 
}else{
 
return name[0];
 
return name[0];
 
}
 
}
}, "aTargets": [ 4 ]}, { "sType": "numeric", "aTargets": [0,1],"fnRender": function (obj) {                  
+
}, targets: [ 4 ]}, { type: "numeric", targets: [0,1], 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  pathway_enrichment_table_tools = new TableTools( pathway_enrichment_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"} ]});
 
 
$('#pathway_enrichment_table_export_tool').before(pathway_enrichment_table_tools.dom.container );
 
}else{
 
 
}
 
}
  
Line 65: Line 62:
 
var gostat_on_coexpression_clusters_flag="</html>{{{gostat_on_coexpression_clusters}}}<html>";
 
var gostat_on_coexpression_clusters_flag="</html>{{{gostat_on_coexpression_clusters}}}<html>";
 
//check if this variable exist ,if not then creation of table and export tool causes error
 
//check if this variable exist ,if not then creation of table and export tool causes error
if(gostat_on_coexpression_clusters_flag.indexOf("{{{") == -1) {  
+
if(gostat_on_coexpression_clusters_flag.indexOf("{{{") == -1) {
 
// GOstat results table start
 
// GOstat results table start
var oTable =  $('#gostat_table').dataTable({
+
var oTable =  $('#gostat_table').DataTable({
                "sScrollY": "300px",
+
        dom: 'lfrtip',
                "bScrollCollapse": true,
+
        scrollY: "300px",
"bPaginate": true,
+
        scrollCollapse: true,
"bFilter": true,
+
        pageLength: 10,
"bInfo": true,
+
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
                "iDisplayLength": 10,
+
order: [[0,'asc']],
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
+
columnDefs: [{type: "numeric", targets: [2],
"aaSorting": [[0,'asc']],
+
        render: function ( data, type, row, meta ) {
"aoColumnDefs": [ { "sType": "numeric", "aTargets": [2],"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 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"} ]});
 
 
$('#gostat_table_export_tool').before( oTableTools.dom.container );
 
}else{
 
 
}
 
}
 
// GOstat results table end
 
// GOstat results table end
  
 
// sample ontology enrichment list start
 
// sample ontology enrichment list start
var enrichment_list_cl_table = $('#enrichment_list_cl').dataTable({
+
var enrichment_list_cl_table = $('#enrichment_list_cl').DataTable({
"sScrollY": "300px",
+
        dom: 'lfrti',
                "bScrollCollapse": true,
+
scrollY: "300px",
"bPaginate": true,
+
        scrollCollapse: true,
"bFilter": true,
+
        pageLength: -1,
"bInfo": true,
+
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
                "iDisplayLength": 10,
+
columnDefs: [{ orderable: false, targets: [ 0 ] },  { type: "numeric", targets: [1] }, { width: "50pt", targets: [ 1 ] }],
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
+
order: [[ 1, "asc" ]]
"aoColumnDefs": [{ "bSortable": false, "aTargets": [ 0 ] },  { "sType": "numeric", "aTargets": [1] }, { "sWidth": "50pt", "aTargets": [ 1 ] }],
 
"aaSorting": [[ 1, "asc" ]]
 
 
});
 
});
  
  
var enrichment_list_uberon_table = $('#enrichment_list_uberon').dataTable({
+
var enrichment_list_uberon_table = $('#enrichment_list_uberon').DataTable({
"sScrollY": "300px",
+
        dom: 'lfrti',
                "bScrollCollapse": true,
+
scrollY: "300px",
"bPaginate": true,
+
        scrollCollapse: true,
"bFilter": true,
+
        pageLength: -1,
"bInfo": true,
+
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
                "iDisplayLength": 10,
+
columnDefs: [{ orderable: false, targets: [ 0 ] },  { type: "numeric", targets: [1] }, { width: "50pt", targets: [ 1 ] }],
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
+
order: [[ 1, "asc" ]]
"aoColumnDefs": [{ "bSortable": false, "aTargets": [ 0 ] },  { "sType": "numeric", "aTargets": [1] }, { "sWidth": "50pt", "aTargets": [ 1 ] }],
 
"aaSorting": [[ 1, "asc" ]]
 
 
});
 
});
  
Line 118: Line 105:
  
  
var enrichment_list_disease_table= $('#enrichment_list_doid').dataTable({
+
var enrichment_list_disease_table= $('#enrichment_list_doid').DataTable({
"sScrollY": "300px",
+
        dom: 'lfrti',
                "bScrollCollapse": true,
+
scrollY: "300px",
"bPaginate": true,
+
        scrollCollapse: true,
"bFilter": true,
+
        pageLength: -1,
"bInfo": true,
+
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
                "iDisplayLength": 10,
+
columnDefs: [{ orderable: false, targets: [ 0 ] },  { type: "numeric", targets: [1] }, { width: "50pt", targets: [ 1 ] }],
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
+
order: [[ 1, "asc" ]]
"aoColumnDefs": [{ "bSortable": false, "aTargets": [ 0 ] },  { "sType": "numeric", "aTargets": [1] }, { "sWidth": "50pt", "aTargets": [ 1 ] }],
 
"aaSorting": [[ 1, "asc" ]]
 
 
});
 
});
  
Line 141: Line 126:
 
}
 
}
  
var tfbs_overexpression_table = $('#tfbs_overexpression_table').dataTable({
+
var tfbs_overexpression_table = $('#tfbs_overexpression_table').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"]],
+
data: data,
"aaData": data,
+
columns: [{ title: "Motifs", width: "200pt", render: function ( data, type, row, meta ) {var elem = data.split("_"); return "<a href=\"/5/sstar/Novel_motif:"+elem[0].replace('motif', '')+"\">"+data+"</a>";}},{ title: "-log10(p-value)", type: "numeric",render: function ( data, type, row, meta ) {
"aoColumns": [{ "sTitle": "Motifs", "sWidth": "200pt", "fnRender": function ( o, val ) {var elem = o.aData[0].split("_"); return "<a href=\"/resource_browser/Novel_motif:"+elem[0].replace('motif', '')+"\">"+o.aData[0]+"</a>";}},{ "sTitle": "-log10(p-value)", "sType": "numeric","fnRender": function (obj) {                  
+
                   var num =data;
                   var num =obj.aData[obj.iDataColumn];
 
 
                   var num_as_number=Number(num);
 
                   var num_as_number=Number(num);
                   return num_as_number.toFixed(2) ;
+
                   return num_as_number.toFixed(2);
 
}}],
 
}}],
"aaSorting": [[ 1, "desc" ]]
+
order: [[ 1, "desc" ]]
 
});
 
});
  
var tfbs_overexpression_table_tools = new TableTools(tfbs_overexpression_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"} ]});
+
var tfbs_overexpression_jaspar_table= $('#tfbs_overexpression_jaspar').DataTable({
 
+
        dom: 'Blfrtip',
$('#tfbs_overexpression_table_export_tool').before(tfbs_overexpression_table_tools.dom.container );
+
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
 
+
scrollY: "300px",
var tfbs_overexpression_jaspar_table= $('#tfbs_overexpression_jaspar').dataTable({
+
        scrollCollapse: true,
"sScrollY": "300px",
+
        pageLength: 10,
                "bScrollCollapse": true,
+
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
"bPaginate": true,
+
columnDefs: [{ width: "200pt", render: function ( data, type, row, meta ) {return "<a href=\"/5/sstar/JASPAR_motif:"+data+"\">"+data+"</a>";}, targets: [ 0 ] }, {type: "numeric", targets: [ 1 ],render: function ( data, type, row, meta ) {
"bFilter": true,
+
                   var num =data;
"bInfo": true,
 
                "iDisplayLength": 10,
 
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
 
"aoColumnDefs": [{ "sWidth": "200pt", "fnRender": function ( o, val ) {return "<a href=\"/resource_browser/JASPAR_motif:"+o.aData[0]+"\">"+o.aData[0]+"</a>";}, "aTargets": [ 0 ] }, {"sType": "numeric", "aTargets": [ 1 ],"fnRender": function (obj) {                  
 
                   var num =obj.aData[obj.iDataColumn];
 
 
                   var num_as_number=Number(num);
 
                   var num_as_number=Number(num);
                   return num_as_number.toFixed(2) ;
+
                   return num_as_number.toFixed(2);
 
} }],
 
} }],
"aaSorting": [[ 1, "desc" ]]
+
order: [[ 1, "desc" ]]
 
});
 
});
var tfbs_overexpression_jaspar_table_tools = new TableTools(tfbs_overexpression_jaspar_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"} ]});
 
 
$('#tfbs_overexpression_jaspar_table_export_tool').before(tfbs_overexpression_jaspar_table_tools.dom.container );
 
 
// tfbs results table end
 
// tfbs results table end
  
 
// tf chipseq results table start
 
// tf chipseq results table start
var tfbs_chipseq_enrich_table=$('#tf_chipseq_enrich').dataTable({
+
if($('#tf_chipseq_enrich')[0]){
"sScrollY": "300px",
+
    var tfbs_chipseq_enrich_table=$('#tf_chipseq_enrich').DataTable({
                "bScrollCollapse": true,
+
        dom: 'Blfrtip',
"bPaginate": true,
+
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
"bFilter": true,
+
scrollY: "300px",
"bInfo": true,
+
        scrollCollapse: true,
                "iDisplayLength": 10,
+
        pageLength: 10,
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
+
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
"aaSorting": [[4,'asc']],
+
order: [[4,'asc']],
"aoColumnDefs": [{"fnRender": function ( o, val ) {var elem = o.aData[0].split("#"); return "<a href=\"/resource_browser/EntrezGene:"+elem[1]+"\">"+elem[0]+"</a>";}, "aTargets": [ 0 ]}, { "sWidth": "150px", "sType": "numeric", "aTargets": [2],"fnRender": function (obj) {                     
+
columnDefs: [{render: function ( data, type, row, meta ) {var elem = data.split("#"); return "<a href=\"/5/sstar/EntrezGene:"+elem[1]+"\">"+elem[0]+"</a>";}, targets: [ 0 ]}, { width: "150px", type: "numeric", targets: [2],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");
} },{  "sType": "numeric", "aTargets": [3],"fnRender": function (obj) {                  
+
} },{  type: "numeric", targets: [3],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");
} },{"sType": "numeric", "aTargets": [4],"fnRender": function (obj) {                  
+
} },{type: "numeric", targets: [4],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");
 
}}]
 
}}]
 +
    });
 +
}
 +
// tf chipseq results table end
 
});
 
});
var tfbs_chipseq_enrich_table_tools = new TableTools(tfbs_chipseq_enrich_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"} ]});
 
 
$('#tf_chipseq_enrich_table_export_tool').before(tfbs_chipseq_enrich_table_tools.dom.container );
 
// tf chipseq results table end
 
} );
 
 
</script>
 
</script>
 
</html>
 
</html>
Line 213: Line 187:
  
 
Full id: [[full_id::{{{full_id}}}]]
 
Full id: [[full_id::{{{full_id}}}]]
{{#set:id={{{id}}}}}
+
{{#set:id={{{id}}}
 +
}}
 
{{#set:cp_member_count={{#ask:[[Category:FFCP]][[Coexpression_cluster_id::{{{id}}}]]|format=count}}}}
 
{{#set:cp_member_count={{#ask:[[Category:FFCP]][[Coexpression_cluster_id::{{{id}}}]]|format=count}}}}
 
{{#ifeq:{{#pos:{{PAGENAME}}|C}}|0
 
{{#ifeq:{{#pos:{{PAGENAME}}|C}}|0
Line 221: Line 196:
  
 
== Phase1 CAGE Peaks ==
 
== Phase1 CAGE Peaks ==
<span id="ffcp_list_table_export_tool"></span>
+
{{#ask:[[Category:FFCP]][[FFCP_PHASE2:+]][[Species::Human (Homo sapiens)]][[Coexpression_cluster_id::{{{id}}}]]|?Short_description|format=table|class=ffcp_list stripe cell-border order-column compact|headers=hide|searchlabel= ...further results|limit=20000}}
{{#ask:[[Category:FFCP]][[Species::Human (Homo sapiens)]][[Coexpression_cluster_id::{{{id}}}]]|?Short_description|format=ttable|class=ffcp_list|limit=20000}}
 
 
<br>
 
<br>
  
Line 229: Line 203:
 
<br>
 
<br>
 
<br>link to source dataset
 
<br>link to source dataset
<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_modules.tar.gz  data]
+
<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_modules.tar.gz  data]
 
}}
 
}}
 
----
 
----
{{#if:{{{pathway_enrichment}}}|<span id="pathway_enrichment_table_export_tool"></span>
+
{{#if:{{{pathway_enrichment|}}}|<span id="pathway_enrichment_table_export_tool"></span>
<table class="pathway_enrichment"><html><thead></html>
+
<table class="pathway_enrichment stripe cell-border order-column compact"><html><thead></html>
 
<tr><th>p.value</th><th>FDR</th><th>nGenes</th><th>nPathway</th><th>Name</th></tr>
 
<tr><th>p.value</th><th>FDR</th><th>nGenes</th><th>nPathway</th><th>Name</th></tr>
 
<html></thead><tbody></html>
 
<html></thead><tbody></html>
{{#if:{{{#arraymap:{{{pathway_enrichment}}}}}}|
 
 
{{#arraymap:{{{pathway_enrichment}}}|!|$
 
{{#arraymap:{{{pathway_enrichment}}}|!|$
 
|<tr><td>{{#replace:$|;|</td><td>}}</td></tr>
 
|<tr><td>{{#replace:$|;|</td><td>}}</td></tr>
|}}|test}}
+
|}}
 
<html></tbody></html></table>
 
<html></tbody></html></table>
 
|No results for this coexpression}}
 
|No results for this coexpression}}
Line 245: Line 218:
 
{{Fontsize|3|Enriched Gene Ontology terms on this co-expression cluster}}{{#info:<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner
 
{{Fontsize|3|Enriched Gene Ontology terms on this co-expression cluster}}{{#info:<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner
 
<br><br>link to source dataset
 
<br><br>link to source dataset
<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_GOstats.tar.gz  data]
+
<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_GOstats.tar.gz  data]
 
}}
 
}}
 
----
 
----
Line 251: Line 224:
 
|Human (Homo sapiens)=
 
|Human (Homo sapiens)=
 
{{#ifeq:{{#sub:{{{gostat_on_coexpression_clusters}}}|0|2}}|GO|<span id="gostat_table_export_tool"></span>
 
{{#ifeq:{{#sub:{{{gostat_on_coexpression_clusters}}}|0|2}}|GO|<span id="gostat_table_export_tool"></span>
<table id="gostat_table"><html><thead></html><tr><th>GO ID</th><th>GO name</th><th>FDR corrected p-value</th></tr><html></thead><tbody></html>
+
<table id="gostat_table" class="stripe cell-border order-column compact"><html><thead></html><tr><th>GO ID</th><th>GO name</th><th>FDR corrected p-value</th></tr><html></thead><tbody></html>
 
<tr>
 
<tr>
 
{{#arraymap:{{{gostat_on_coexpression_clusters}}}|$|$
 
{{#arraymap:{{{gostat_on_coexpression_clusters}}}|$|$
Line 274: Line 247:
 
{{Fontsize|3|Enriched sample ontology terms on this co-expression cluster}}{{#info:<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji  
 
{{Fontsize|3|Enriched sample ontology terms on this co-expression cluster}}{{#info:<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji  
 
<br><br>links to source dataset<br><br>
 
<br><br>links to source dataset<br><br>
{{#if:{{{ontology_enrichment_celltype}}}|[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/mcl_hg19_clusters_relative_exp_enrichment_cell_type.txt.gz  cell_data]|}}<br>
+
{{#if:{{{ontology_enrichment_celltype}}}|[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/mcl_hg19_clusters_relative_exp_enrichment_cell_type.txt.gz  cell_data]|}}<br>
{{#if:{{{ontology_enrichment_uberon}}}|[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/mcl_hg19_clusters_relative_exp_enrichment_uberon.txt.gz  uberon_data]|}}<br>
+
{{#if:{{{ontology_enrichment_uberon}}}|[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/mcl_hg19_clusters_relative_exp_enrichment_uberon.txt.gz  uberon_data]|}}<br>
{{#if:{{{ontology_enrichment_disease}}}|[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/mcl_hg19_clusters_relative_exp_enrichment_disease.txt.gz  disease_data]|}}<br>
+
{{#if:{{{ontology_enrichment_disease}}}|[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/mcl_hg19_clusters_relative_exp_enrichment_disease.txt.gz  disease_data]|}}<br>
 
}}
 
}}
 
----
 
----
 
{{#if:{{{ontology_enrichment_celltype}}}|
 
{{#if:{{{ontology_enrichment_celltype}}}|
 
<div style="float:left;width:33%;">
 
<div style="float:left;width:33%;">
<table id="enrichment_list_cl"><caption class="table_title">Cell Type</caption><html><thead></html>
+
<table id="enrichment_list_cl" class="stripe cell-border order-column compact"><caption class="table_title">Cell Type</caption><html><thead></html>
 
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
 
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
 
<html></thead><tbody></html>
 
<html></thead><tbody></html>
Line 291: Line 264:
 
}}{{#if:{{{ontology_enrichment_uberon}}}|
 
}}{{#if:{{{ontology_enrichment_uberon}}}|
 
<div style="float:left;width:33%;">
 
<div style="float:left;width:33%;">
<table id="enrichment_list_uberon"><caption class="table_title">Uber Anatomy</caption><html><thead></html>
+
<table id="enrichment_list_uberon" class="stripe cell-border order-column compact"><caption class="table_title">Uber Anatomy</caption><html><thead></html>
 
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
 
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
 
<html></thead><tbody></html>{{#arraymap:{{{ontology_enrichment_uberon}}}|;|$
 
<html></thead><tbody></html>{{#arraymap:{{{ontology_enrichment_uberon}}}|;|$
Line 300: Line 273:
 
}}{{#if:{{{ontology_enrichment_disease}}}|
 
}}{{#if:{{{ontology_enrichment_disease}}}|
 
<div style="float:left;width:33%;">
 
<div style="float:left;width:33%;">
<table id="enrichment_list_doid"><caption class="table_title">Disease</caption><html><thead></html>
+
<table id="enrichment_list_doid" class="stripe cell-border order-column compact"><caption class="table_title">Disease</caption><html><thead></html>
 
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
 
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
 
<html></thead><tbody></html>{{#arraymap:{{{ontology_enrichment_disease}}}|;|$
 
<html></thead><tbody></html>{{#arraymap:{{{ontology_enrichment_disease}}}|;|$
Line 315: Line 288:
 
|{{Fontsize|3|Overrepresented TFBS (DNA) motifs on this co-expression cluster}}{{#info:<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>
 
|{{Fontsize|3|Overrepresented TFBS (DNA) motifs on this co-expression cluster}}{{#info:<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>
 
link to source data <br> Novel motifs <br>
 
link to source data <br> Novel motifs <br>
[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19.novel_motif.coexpression_clusters_overrepresentation.txt.gz data] <br>
+
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19.novel_motif.coexpression_clusters_overrepresentation.txt.gz data] <br>
 
<br> Jaspar motifs <br>
 
<br> Jaspar motifs <br>
[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz data]
+
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz data]
 
}}
 
}}
 
----
 
----
 
{{Fontsize|3|Novel motifs}}{{#if:{{{tfbs_overrepresentation_for_novel_motifs}}}
 
{{Fontsize|3|Novel motifs}}{{#if:{{{tfbs_overrepresentation_for_novel_motifs}}}
|<span id="tfbs_overexpression_table_export_tool"></span><table id="tfbs_overexpression_table"></table>
+
|<span id="tfbs_overexpression_table_export_tool"></span><table id="tfbs_overexpression_table" class="stripe cell-border order-column compact"></table>
 
|No results for this section
 
|No results for this section
 
}} <br><br>
 
}} <br><br>
 
{{Fontsize|3|JASPAR motifs}}{{#if:Summary:{{{tfbs_overrepresentation_jaspar}}}
 
{{Fontsize|3|JASPAR motifs}}{{#if:Summary:{{{tfbs_overrepresentation_jaspar}}}
|<span id="tfbs_overexpression_jaspar_table_export_tool"></span><table id="tfbs_overexpression_jaspar"><html><thead></html>
+
|<span id="tfbs_overexpression_jaspar_table_export_tool"></span><table id="tfbs_overexpression_jaspar" class="stripe cell-border order-column compact"><html><thead></html>
 
<tr><th>Motifs</th><th>-log10(p-value)</th></tr><html></thead><tbody></html>
 
<tr><th>Motifs</th><th>-log10(p-value)</th></tr><html></thead><tbody></html>
 
<tr><td>
 
<tr><td>
Line 339: Line 312:
 
{{Fontsize|3|ENCODE TF ChIP-seq peak enrichment analysis}}{{#info: <b>Summary:</b> 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><b>Analyst:</b> Erik Arner
 
{{Fontsize|3|ENCODE TF ChIP-seq peak enrichment analysis}}{{#info: <b>Summary:</b> 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><b>Analyst:</b> Erik Arner
 
<br><br>link to source dataset<br>
 
<br><br>link to source dataset<br>
<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/ENCODE%20TF%20ChIP-seq%20peak%20enrichment%20analysis/coexprclusterencode.filtered.csv.gz  data]
+
<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/ENCODE%20TF%20ChIP-seq%20peak%20enrichment%20analysis/coexprclusterencode.filtered.csv.gz  data]
 
}}  
 
}}  
 
----
 
----
 
{{#if: {{#pos:{{{tf_chipseq_enrich}}}|;}}  
 
{{#if: {{#pos:{{{tf_chipseq_enrich}}}|;}}  
 
|(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)<span id="tf_chipseq_enrich_table_export_tool"></span>  
 
|(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)<span id="tf_chipseq_enrich_table_export_tool"></span>  
<table id="tf_chipseq_enrich"><html><thead></html><tr><th>TF</th><th>#promoters</th><th>Enrichment</th><th>p-value</th><th>q-value</th></tr><html></thead><tbody></html>
+
<table id="tf_chipseq_enrich" class="stripe cell-border order-column compact"><html><thead></html><tr><th>TF</th><th>#promoters</th><th>Enrichment</th><th>p-value</th><th>q-value</th></tr><html></thead><tbody></html>
 
{{#arraymap:{{{tf_chipseq_enrich}}}|!|$
 
{{#arraymap:{{{tf_chipseq_enrich}}}|!|$
 
|{{#set:tf_chipseq_enrich={{#explode:$|#|1}}}}<tr><td>{{#replace:{{#replace:$|;|</td><td>}}|:|</td><td>}}</td></tr>
 
|{{#set:tf_chipseq_enrich={{#explode:$|#|1}}}}<tr><td>{{#replace:{{#replace:$|;|</td><td>}}|:|</td><td>}}</td></tr>
Line 354: Line 327:
 
<br>
 
<br>
 
{{Fontsize|3|Relative expression of the co-expression cluster}}{{#info:<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br>   
 
{{Fontsize|3|Relative expression of the co-expression cluster}}{{#info:<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br>   
[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/coexpression_DPI_cluster_scores_median_human_Aug3_2012.txt.gz  data]}}
+
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/coexpression_DPI_cluster_scores_median_human_Aug3_2012.txt.gz  data]}}
 
----
 
----
 
{{#ifexpr:{{#sub:{{{id}}}|1}} < 306|<html><script type="text/javascript">
 
{{#ifexpr:{{#sub:{{{id}}}|1}} < 306|<html><script type="text/javascript">
Line 364: Line 337:
 
data.push([ffsample[i1],values[i1]]);
 
data.push([ffsample[i1],values[i1]]);
 
}
 
}
 
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{{#array_recordprops:coexpression_dpi_cluster_scores_median
 
{{#array_recordprops:coexpression_dpi_cluster_scores_median
Line 398: Line 372:
 
|This analysis result is provided for C0 - C305 clusters.
 
|This analysis result is provided for C0 - C305 clusters.
 
}}
 
}}
 +
  
 
[[Category:Coexpression_clusters]]
 
[[Category:Coexpression_clusters]]

Latest revision as of 02:59, 22 September 2021


Full id: {{{full_id}}}



Phase1 CAGE Peaks


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No results for this coexpression

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>


Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen




ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> 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><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


Expression error: Unrecognized punctuation character "{".