Template:Coexpression clusters: Difference between revisions
From FANTOM5_SSTAR
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{{Loading|loadingimage=sprites.gif}}<html> | {{Loading|loadingimage=sprites.gif}}<html> | ||
<script type="text/javascript" src="/ | <script type="text/javascript" src="/5/sstar/rb_js/datatables/media/js/jquery.dataTables.min.js"></script> | ||
<script type="text/javascript" src="/ | <script type="text/javascript" src="/5/sstar/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script> | ||
<script type="text/javascript" src="/ | <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 "/ | @import "/5/sstar/rb_js/datatables/media/css/jquery.dataTables.css"; | ||
@import "/ | @import "/5/sstar/rb_js/datatables/extras/TableTools/media/css/TableTools.css"; | ||
.table_title{ | .table_title{ | ||
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// 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": "/ | var ffcp_list_table_tools = new TableTools( ffcp_list_table, {"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"} ]}); | ||
$('#ffcp_list_table_export_tool').before(ffcp_list_table_tools.dom.container ); | $('#ffcp_list_table_export_tool').before(ffcp_list_table_tools.dom.container ); | ||
// FFCP list end | // FFCP list end | ||
if($('.pathway_enrichment').size()>0){ | |||
if( | |||
// Pathway enrichment analysis start | // Pathway enrichment analysis start | ||
var pathway_enrichment_table =$('.pathway_enrichment').dataTable({ | var pathway_enrichment_table =$('.pathway_enrichment').dataTable({ | ||
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}); | }); | ||
var pathway_enrichment_table_tools = new TableTools( pathway_enrichment_table, {"sSwfPath": "/ | var pathway_enrichment_table_tools = new TableTools( pathway_enrichment_table, {"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"} ]}); | ||
$('#pathway_enrichment_table_export_tool').before(pathway_enrichment_table_tools.dom.container ); | $('#pathway_enrichment_table_export_tool').before(pathway_enrichment_table_tools.dom.container ); | ||
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}); | }); | ||
var oTableTools = new TableTools( oTable, {"sSwfPath": "/ | 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"} ]}); | ||
$('#gostat_table_export_tool').before( oTableTools.dom.container ); | $('#gostat_table_export_tool').before( oTableTools.dom.container ); | ||
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"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=\"/ | "aoColumns": [{ "sTitle": "Motifs", "sWidth": "200pt", "fnRender": function ( o, val ) {var elem = o.aData[0].split("_"); return "<a href=\"/5/sstar/Novel_motif:"+elem[0].replace('motif', '')+"\">"+o.aData[0]+"</a>";}},{ "sTitle": "-log10(p-value)", "sType": "numeric","fnRender": function (obj) { | ||
var num =obj.aData[obj.iDataColumn]; | var num =obj.aData[obj.iDataColumn]; | ||
var num_as_number=Number(num); | var num_as_number=Number(num); | ||
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}); | }); | ||
var tfbs_overexpression_table_tools = new TableTools(tfbs_overexpression_table, {"sSwfPath": "/ | var tfbs_overexpression_table_tools = new TableTools(tfbs_overexpression_table, {"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"} ]}); | ||
$('#tfbs_overexpression_table_export_tool').before(tfbs_overexpression_table_tools.dom.container ); | $('#tfbs_overexpression_table_export_tool').before(tfbs_overexpression_table_tools.dom.container ); | ||
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"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=\"/ | "aoColumnDefs": [{ "sWidth": "200pt", "fnRender": function ( o, val ) {return "<a href=\"/5/sstar/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 =obj.aData[obj.iDataColumn]; | ||
var num_as_number=Number(num); | var num_as_number=Number(num); | ||
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"aaSorting": [[ 1, "desc" ]] | "aaSorting": [[ 1, "desc" ]] | ||
}); | }); | ||
var tfbs_overexpression_jaspar_table_tools = new TableTools(tfbs_overexpression_jaspar_table, {"sSwfPath": "/ | var tfbs_overexpression_jaspar_table_tools = new TableTools(tfbs_overexpression_jaspar_table, {"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"} ]}); | ||
$('#tfbs_overexpression_jaspar_table_export_tool').before(tfbs_overexpression_jaspar_table_tools.dom.container ); | $('#tfbs_overexpression_jaspar_table_export_tool').before(tfbs_overexpression_jaspar_table_tools.dom.container ); | ||
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// tf chipseq results table start | // tf chipseq results table start | ||
var tfbs_chipseq_enrich_table=$('#tf_chipseq_enrich').dataTable({ | var tfbs_chipseq_enrich_table=$('#tf_chipseq_enrich').dataTable({ | ||
"sScrollY": "300px", | "sScrollY": "300px", | ||
"bScrollCollapse": true, | "bScrollCollapse": true, | ||
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"aLengthMenu": [[10, 50, -1], [10, 50, "All"]], | "aLengthMenu": [[10, 50, -1], [10, 50, "All"]], | ||
"aaSorting": [[4,'asc']], | "aaSorting": [[4,'asc']], | ||
"aoColumnDefs": [{"fnRender": function ( o, val ) {var elem = o.aData[0].split("#"); return "<a href=\"/ | "aoColumnDefs": [{"fnRender": function ( o, val ) {var elem = o.aData[0].split("#"); return "<a href=\"/5/sstar/EntrezGene:"+elem[1]+"\">"+elem[0]+"</a>";}, "aTargets": [ 0 ]}, { "sWidth": "150px", "sType": "numeric", "aTargets": [2],"fnRender": function (obj) { | ||
var num =obj.aData[obj.iDataColumn]; | var num =obj.aData[obj.iDataColumn]; | ||
return exp_converter(num,2,"e") ; | return exp_converter(num,2,"e") ; | ||
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return exp_converter(num,2,"e") ; | return exp_converter(num,2,"e") ; | ||
}}] | }}] | ||
}); | }); | ||
var tfbs_chipseq_enrich_table_tools = new TableTools(tfbs_chipseq_enrich_table, {"sSwfPath": "/ | var tfbs_chipseq_enrich_table_tools = new TableTools(tfbs_chipseq_enrich_table, {"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"} ]}); | ||
$('#tf_chipseq_enrich_table_export_tool').before(tfbs_chipseq_enrich_table_tools.dom.container ); | $('#tf_chipseq_enrich_table_export_tool').before(tfbs_chipseq_enrich_table_tools.dom.container); | ||
// tf chipseq results table end | // tf chipseq results table end | ||
} ); | }); | ||
</script> | </script> | ||
</html> | </html> | ||
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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 | ||
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== Phase1 CAGE Peaks == | == Phase1 CAGE Peaks == | ||
<span id="ffcp_list_table_export_tool"></span> | <span id="ffcp_list_table_export_tool"></span> | ||
{{#ask:[[Category:FFCP]][[Species::Human (Homo sapiens)]][[Coexpression_cluster_id::{{{id}}}]]|?Short_description|format=ttable|class=ffcp_list|limit=20000}} | {{#ask:[[Category:FFCP]][[FFCP_PHASE2:+]][[Species::Human (Homo sapiens)]][[Coexpression_cluster_id::{{{id}}}]]|?Short_description|format=ttable|class=ffcp_list|limit=20000}} | ||
<br> | <br> | ||
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}} | }} | ||
---- | ---- | ||
{{#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"><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> | ||
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var id = obj.aData[ obj.iDataColumn ]; | var id = obj.aData[ obj.iDataColumn ]; | ||
var elems = id.split('.'); | var elems = id.split('.'); | ||
return sReturn = "<a href=\"/ | return sReturn = "<a href=\"/5/sstar/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]; | ||
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}); | }); | ||
var coexpression_dpi_cluster_scores_median_table_export_tools = new TableTools(coexpression_dpi_cluster_scores_median_table, {"sSwfPath": "/ | var coexpression_dpi_cluster_scores_median_table_export_tools = new TableTools(coexpression_dpi_cluster_scores_median_table, {"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"} ]}); | ||
$('#coexpression_dpi_cluster_scores_median_table_export_tool').before(coexpression_dpi_cluster_scores_median_table_export_tools.dom.container ); | $('#coexpression_dpi_cluster_scores_median_table_export_tool').before(coexpression_dpi_cluster_scores_median_table_export_tools.dom.container ); | ||
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|This analysis result is provided for C0 - C305 clusters. | |This analysis result is provided for C0 - C305 clusters. | ||
}} | }} | ||
[[Category:Coexpression_clusters]] | [[Category:Coexpression_clusters]] | ||
Revision as of 14:47, 1 July 2016
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>
| Ontology term | p-value | n |
|---|
| Ontology term | p-value | n |
|---|
| Ontology term | p-value | n |
|---|
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 "{".
