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<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/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" src="/resource_browser/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 "/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/TableToolfs/media/css/TableTools.css";
.table_title{
.table_title{
text-align:left;
text-align:left;
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rexp_median_data.push([rexp_sample[i1], rexp_median_values[i1]]);
rexp_median_data.push([rexp_sample[i1], rexp_median_values[i1]]);
}
}
    $('#coexpression_dpi_cluster_scores_median_table').dataTable({
  var coexpression_dpi_cluster_scores_table =  $('#coexpression_dpi_cluster_scores_median_table').dataTable({
"sScrollY": "300px",
"sScrollY": "300px",
                 "bScrollCollapse": true,
                 "bScrollCollapse": true,
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return sReturn = "<a href=\"/resource_browser/FF:"+elems[2]+"\">"+decodeURIComponent(elems[0])+" "+elems[1]+"</a>";
return sReturn = "<a href=\"/resource_browser/FF:"+elems[2]+"\">"+decodeURIComponent(elems[0])+" "+elems[1]+"</a>";
} },{ "sTitle": "Score", "sType": "numeric" ,"fnRender": function (obj) {
} },{ "sTitle": "Score", "sType": "numeric" ,"fnRender": function (obj) {
                  var num =obj.aData[obj.iDataColumn];
              var num =obj.aData[obj.iDataColumn];
                   return num.toFixed(2) ;
              var numb = new Number(num);
}}],
                   return numb.toFixed(2) ;
"aaSorting": [[ 1, "desc" ]]
} }],
"aaSorting": [[ 1, "desc" ]],
});
});
var coexpression_dpi_cluster_scores_table_tool = new TableTools( coexpression_dpi_cluster_scores_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"} ]});
$('#relative_exp_of_coexp_table_button').before(coexpression_dpi_cluster_scores_table_tool.dom.container );


// ontology enrichment table
// ontology enrichment table
$('.enrichment_list').dataTable({
$('.enrichment_list').dataTable({
"sScrollY": "300px",
"sScrollY": "300px",
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"aaSorting": [[ 1, "asc" ]]
"aaSorting": [[ 1, "asc" ]]
});
});


// ffcp list
// ffcp list
$('.ffcp_list').dataTable();
var ffcp_list_table=$('.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"} ]});
$('#ffcp_list_table_export_tool').before(ffcp_list_table_tools.dom.container );


} );
} );
</script>
</script>
</html>
</html>
 
<br>


== Phase1 CAGE Peaks ==
== Phase1 CAGE Peaks ==
 
<span id="ffcp_list_table_export_tool"></span>
{{#ask:[[Category:FFCP]][[Species::Mouse (Mus musculus)]][[MCL_coexpression_id::{{PAGENAME}}]]|?Short_description|format=ttable|class=ffcp_list|limit=20000}}
{{#ask:[[Category:FFCP]][[Species::Mouse (Mus musculus)]][[MCL_coexpression_id::{{PAGENAME}}]]|?Short_description|format=ttable|class=ffcp_list|limit=20000}}
<br>


{{Fontsize|3|Enriched pathways on this co-expression cluster}}{{#info:<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>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_modules.tar.gz  data]
}}
----
{{#if:{{{pathway_enrichment}}}|
<html>
<script type="text/javascript">
$(document).ready(function() {
  var pathway_enrichment_table= $('#pathway_enrichment').dataTable({
"sScrollY": "300px",
                "bScrollCollapse": true,
"bPaginate": true,
"bFilter": true,
"bInfo": true,
                "iDisplayLength": 10,
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
"aaSorting": [[0,'asc']],
"aoColumnDefs": [{"fnRender": function ( o, val ) {
var name = o.aData[4].split(":");
if(name[0].indexOf("KEGG") != -1){
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){
return "<a href=\"http://www.wikipathways.org/index.php/Pathway:"+name[1]+"\">"+name[0]+"</a>";
}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>";
}else if(name[0].indexOf("Netpath") != -1){
return "<a href=\"http://www.netpath.org/pathways?path_id="+name[1]+"\">"+name[0]+"</a>";
}else if(name[0].indexOf("Static Module") != -1){
return "<a href=\"http://genomebiology.com/content/11/5/R53\">"+name[0]+"</a>";
}else{
return name[0];
}
}, "aTargets": [ 2,3,4 ]}, { "sType": "numeric", "aTargets": [0,1],"fnRender": function (obj) {                   
                  var num =obj.aData[obj.iDataColumn];
                  return exp_converter(num,2,"e") ;
} }]
});
var pathway_enrichment_table_tool = 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"} ]});


== GOStat results on Coexpression cluster ==
$('#pathway_enrichment_table_tool_button').before( pathway_enrichment_table_tool.dom.container );
{{#info:The results for GOStat analysis on co-expressed clusters("All" category). <br>Analyst: Erik Arner}}
});
</script>
</html>
<span id="pathway_enrichment_table_tool_button"></span>
<table id="pathway_enrichment"><html><thead></html><tr><th>p.value</th><th>FDR</th><th>nGenes</th><th>nPathway</th><th>Name</th></tr><html></thead><tbody></html>
{{#arraymap:{{{pathway_enrichment}}}|!|$
|<tr><td>{{#replace:$|;|</td><td>}}</td></tr>
|}}
<html></tbody></html></table>
|No results for this coexpression}}
<br><br>
{{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>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_GOstats.tar.gz  data]
}}
----
{{#if:{{{gostat_on_MCL_coexpression}}}|
{{#if:{{{gostat_on_MCL_coexpression}}}|
<html>
<html>
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// GOstat results table start
// GOstat results table start
     var oTable =  $('#gostat_table').dataTable({
     var oTable =  $('#gostat_table').dataTable({
"sScrollY": "300px",
                "sScrollY": "300px",
                 "bScrollCollapse": true,
                 "bScrollCollapse": true,
"bPaginate": true,
"bPaginate": true,
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                 "iDisplayLength": 10,
                 "iDisplayLength": 10,
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
"aoColumnDefs": [ { "sType": "numeric", "aTargets": [2] }],
"aoColumnDefs": [ { "sType": "numeric", "aTargets": [2],"fnRender": function (obj) {
                  var num =obj.aData[obj.iDataColumn];
                  return exp_converter(num,2,"e");
} }],
"aaSorting": [[2,'asc']]
"aaSorting": [[2,'asc']]
});
});
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</script>
</script>
</html>
</html>


<span id="gostat_table_export_tool"></span>
<span id="gostat_table_export_tool"></span>
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|no results for this coexpression
|no results for this coexpression
}}
}}
 
<br><br>
 
{{Fontsize|3|Relative expression of the co-expression cluster over median }}{{#info: <br>Analyst: }}
 
----
== Relative expression of the co-expression cluster -Median- ==
<div id="relative_exp_of_coexp_table_button"></div><br>
{{#info: <br>Analyst: }}
<table id="coexpression_dpi_cluster_scores_median_table"></table>
<table id="coexpression_dpi_cluster_scores_median_table"></table>
{{#array_recordprops:coexpression_dpi_cluster_scores_median
{{#array_recordprops:coexpression_dpi_cluster_scores_median
Line 121: Line 189:
|{{{coexpression_dpi_cluster_scores_median}}}
|{{{coexpression_dpi_cluster_scores_median}}}
}}
}}
 
<br><br>
 
{{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
== Ontology enrichment ==
<br><br>links to source dataset<br><br>
{{#info: <br>Analyst: }}
{{#if:{{{ontology_enrichment_celltype}}}|[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/mcl_mm9_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_mm9_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_mm9_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 class="enrichment_list"><caption class="table_title">Cell Type</caption><html><thead></html>
<table class="enrichment_list" id="enrichment_list_cell_type_table"><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><tr><td>
<html></thead><tbody></html>
{{#arraymap:{{{ontology_enrichment_celltype}}}|;|$
{{#arraymap:{{{ontology_enrichment_celltype}}}|;|$
|{{#set:MCL_coexpression_mm9_ontology_enrichment_celltype={{#replace:$|!|;}}}}[[{{#explode:$|!|0}}|{{#show:{{#explode:$|!|0}}|?name}}]]</td><td>{{#explode:$|!|1}}</td><td>{{#explode:$|!|2}}
|{{#ifexist:{{#explode:$|!|0}}|<tr><td>[[{{#explode:$|!|0}}|{{#show:{{#explode:$|!|0}}|?name}}]]</td><td>{{#explode:$|!|1}}</td><td>{{#explode:$|!|2}}</td></tr>| }}
|</td></tr><tr><td>}}
|
</td></tr>
}}
<html></tbody></html></table>
<html></tbody></html></table>
</div>
</div>
}}{{#if:{{{ontology_enrichment_uberon}}}|
}}{{#if:{{{ontology_enrichment_uberon}}}|
<div style="float:left;width:33%;">
<div style="float:left;width:33%;">
<table class="enrichment_list"><caption class="table_title">Uber Anatomy</caption><html><thead></html>
<table class="enrichment_list" id="enrichment_list_uberon_table"><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><tr><td>
<html></thead><tbody></html>
{{#arraymap:{{{ontology_enrichment_uberon}}}|;|$
{{#arraymap:{{{ontology_enrichment_uberon}}}|;|$
|{{#set:MCL_coexpression_mm9_ontology_enrichment_uberon={{#replace:$|!|;}}}}[[{{#explode:$|!|0}}|{{#show:{{#explode:$|!|0}}|?name}}]]</td><td>{{#explode:$|!|1}}</td><td>{{#explode:$|!|2}}
|{{#ifexist:{{#explode:$|!|0}}|<tr><td>[[{{#explode:$|!|0}}|{{#show:{{#explode:$|!|0}}|?name}}]]</td><td>{{#explode:$|!|1}}</td><td>{{#explode:$|!|2}}</td></tr>| }}
|</td></tr><tr><td>}}
|}}
</td></tr>
<html></tbody></html></table>
<html></tbody></html></table>
</div>
</div>
}}{{#if:{{{ontology_enrichment_disease}}}|
}}{{#if:{{{ontology_enrichment_disease}}}|
<div style="float:left;width:33%;">
<div style="float:left;width:33%;">
<table class="enrichment_list"><caption class="table_title">Disease</caption><html><thead></html>
<table class="enrichment_list" id="enrichment_list_disease_table"><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><tr><td>
<html></thead><tbody></html>
{{#arraymap:{{{ontology_enrichment_disease}}}|;|$
{{#arraymap:{{{ontology_enrichment_disease}}}|;|$
|{{#set:MCL_coexpression_mm9_ontology_enrichment_disease={{#replace:$|!|;}}}}[[{{#explode:$|!|0}}|{{#show:{{#explode:$|!|0}}|?name}}]]</td><td>{{#explode:$|!|1}}</td><td>{{#explode:$|!|2}}
|{{#ifexist:{{#explode:$|!|0}}|<tr><td>[[{{#explode:$|!|0}}|{{#show:{{#explode:$|!|0}}|?name}}]]</td><td>{{#explode:$|!|1}}</td><td>{{#explode:$|!|2}}</td></tr>| }}
|</td></tr><tr><td>}}
|}}
</td></tr>
<html></tbody></html></table>
<html></tbody></html></table>
</div>
</div>
}}
}}
<div style="clear:both;"></div>
<div style="clear:both;"></div>
 
<br>
 
{{Fontsize|3|TFBS overrepresentation}}{{#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>
== TFBS overrepresentation ==
link to source data <br> Novel motifs <br>
{{#info:The values shown are the p-values for over-representation of the motif in this co-expression cluster. So a small p-value means a strong over-representation. <br>Analyst: Michiel de Hoon}}
[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9.novel_motif.coexpression_clusters_overrepresentation.txt.gz data] <br>
<br> Jaspar motifs <br>
[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz data]
}}
----
<html>
<html>
<script type="text/javascript">
<script type="text/javascript">
Line 174: Line 248:
}
}


  var tfbs_overexpression_novel_table_obj= $('#tfbs_overexpression_table').dataTable({
var tfbs_overexpression_novel_table_obj= $('#tfbs_overexpression_table').dataTable({
//"aaData": [["one", 1],["two", 3],["three", 0]],
"sScrollY": "300px",
"sScrollY": "300px",
                 "bScrollCollapse": true,
                 "bScrollCollapse": true,
Line 182: Line 257:
                 "iDisplayLength": 10,
                 "iDisplayLength": 10,
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
"aaData": data,
                "aaData": data,
"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)" }],
                "aoColumns": [{ "sTitle": "Motifs", "sWidth": "300pt", "bSortable": true, "fnRender": function(obj) {
"aaSorting": [[ 1, "desc" ]]
var id = obj.aData[ obj.iDataColumn ];
                var elems = id.split('_')[0];
                            var motif_id=elems.substr(5,elems.length);
  return sReturn = "<a href=\"/resource_browser/Novel_motif:"+motif_id+"\">"+decodeURIComponent(id)+"</a>";
              } },
                            { "sTitle": "-log10(p-value)","sType": "numeric","fnRender": function (obj) {                   
                  var num =obj.aData[obj.iDataColumn];
                  var num_as_number=Number(num);
                  return num_as_number.toFixed(2) ;
} }],
                "aaSorting": [[ 1, "desc" ]]
});
});
  var tfbs_overexpression_novel_table_objtool = new TableTools(  tfbs_overexpression_novel_table_obj, {"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_novel_table_objtool = new TableTools(  tfbs_overexpression_novel_table_obj, {"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_novel_table_button').before( tfbs_overexpression_novel_table_objtool.dom.container );
$('#tfbs_overexpression_novel_table_button').before( tfbs_overexpression_novel_table_objtool.dom.container );


  var tfbs_overexpression_jaspar_table_obj=$('#tfbs_overexpression_jaspar').dataTable({
tfbs_overexpression_jaspar_table_obj=$('#tfbs_overexpression_jaspar').dataTable({
"sScrollY": "300px",
"sScrollY": "300px",
                 "bScrollCollapse": true,
                 "bScrollCollapse": true,
Line 198: Line 283:
                 "iDisplayLength": 10,
                 "iDisplayLength": 10,
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
"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 ] }],
"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);
                  return num_as_number.toFixed(2) ;
} }],
"aaSorting": [[ 1, "desc" ]]
"aaSorting": [[ 1, "desc" ]]
});
});
var tfbs_overexpression_jaspar_table_objtool = new TableTools( tfbs_overexpression_jaspar_table_obj, {"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_objtool = new TableTools( tfbs_overexpression_jaspar_table_obj, {"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_button').before(tfbs_overexpression_jaspar_table_objtool.dom.container );
$('#tfbs_overexpression_jaspar_table_button').before(tfbs_overexpression_jaspar_table_objtool.dom.container );
});
});
</script>
</script>
</html><br>
</html>
=== Novel motifs ===
{{Fontsize|3|Novel motifs}}
<table id="tfbs_overexpression_table"></table> <br><br>
<div id="tfbs_overexpression_novel_table_button"></div><br>
=== JASPAR motifs ===
<table id="tfbs_overexpression_table"></table><br><br>
{{Fontsize|3|JASPAR motifs}}
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[[Category:MCL_coexpression_mm9]]
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Revision as of 10:30, 8 April 2014


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

p.valueFDRnGenesnPathwayName
{{{pathway_enrichment}}}



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

GO IDGO nameFDR corrected p-value
{{{gostat_on_MCL_coexpression}}}



Relative expression of the co-expression cluster over median <br>Analyst:


"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

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


TFBS overrepresentation<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>data <br><br> Jaspar motifs <br>data

Novel motifs




JASPAR motifs


Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}

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