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{{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="/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/TableTools/media/css/TableTools.css";
 
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text-align:left;
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Line 9: Line 13:
}
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</style>
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<script type="text/javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.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">
<script type="text/javascript">
var aDataSet =
[
</html>
{{#ask:[[Category:FFCP]][[Coexpression_cluster_id::{{{id}}}]]|mainlabel=-|?id|?Short_description|format=template|template=Singlecolumn_to_array|sep=,|limit=20000}}
<html>
];
$(document).ready(function() {
$(document).ready(function() {
// FFCP list start
// FFCP list start
$('.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"} ]});
 
$('#ffcp_list_table_export_tool').before(ffcp_list_table_tools.dom.container );
// FFCP list end
// FFCP list end
var pathway_enrichment_flag="</html>{{{pathway_enrichment}}}<html>";
if(pathway_enrichment_flag.length>5){
// Pathway enrichment analysis start
var pathway_enrichment_table =$('.pathway_enrichment').dataTable({
"sScrollY": "300px",
                "bScrollCollapse": true,
"bPaginate": true,
"bFilter": true,
"bInfo": true,
                "iDisplayLength": 10,
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
"aaSorting": [[1,'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": [ 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_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{
}
// Pathway enrichment analysis end
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
if(gostat_on_coexpression_clusters_flag.indexOf("{{{") == -1) { 
// GOstat results table start
var oTable =  $('#gostat_table').dataTable({
                "sScrollY": "300px",
                "bScrollCollapse": true,
"bPaginate": true,
"bFilter": true,
"bInfo": true,
                "iDisplayLength": 10,
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
"aaSorting": [[0,'asc']],
"aoColumnDefs": [ { "sType": "numeric", "aTargets": [2],"fnRender": function (obj) {
                  var num =obj.aData[obj.iDataColumn];
                  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


// sample ontology enrichment list start
// sample ontology enrichment list start
$('.enrichment_list').dataTable({
var enrichment_list_cl_table = $('#enrichment_list_cl').dataTable({
"sScrollY": "300px",
"sScrollY": "300px",
                 "bScrollCollapse": true,
                 "bScrollCollapse": true,
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"aaSorting": [[ 1, "asc" ]]
"aaSorting": [[ 1, "asc" ]]
});
});
var enrichment_list_uberon_table = $('#enrichment_list_uberon').dataTable({
"sScrollY": "300px",
                "bScrollCollapse": true,
"bPaginate": true,
"bFilter": true,
"bInfo": true,
                "iDisplayLength": 10,
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
"aoColumnDefs": [{ "bSortable": false, "aTargets": [ 0 ] },  { "sType": "numeric", "aTargets": [1] }, { "sWidth": "50pt", "aTargets": [ 1 ] }],
"aaSorting": [[ 1, "asc" ]]
});
var enrichment_list_disease_table= $('#enrichment_list_doid').dataTable({
"sScrollY": "300px",
                "bScrollCollapse": true,
"bPaginate": true,
"bFilter": true,
"bInfo": true,
                "iDisplayLength": 10,
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
"aoColumnDefs": [{ "bSortable": false, "aTargets": [ 0 ] },  { "sType": "numeric", "aTargets": [1] }, { "sWidth": "50pt", "aTargets": [ 1 ] }],
"aaSorting": [[ 1, "asc" ]]
});
// sample ontology enrichment list end
// sample ontology enrichment list end


// GOstat results table start
// tfbs results table start
var oTable = $('#gostat_table').dataTable({
var motifs = ['motif1_TCGNAG','motif2_GCTGGAGG','motif3_CGCTNA','motif4_TGTCTA','motif5_CAGTGT','motif6_AAGACT','motif7_CGNATC','motif8_CCATGN','motif9_ANGGCT','motif10_SCGGAGASN','motif11_GCGANT','motif12_ACTAAG','motif13_GAGGATGCK','motif14_TCNACG','motif15_ACTGTG','motif16_ACCAG','motif17_CGCTAN','motif18_CATCAG','motif19_GYTGGMC','motif20_TGNAGC','motif21_TCTTGA','motif22_GGMCTG','motif23_CGCNAT','motif24_AGAACT','motif25_GATCCN','motif26_CTCCGCAGTA','motif27_CCTGCA','motif28_CGTNCA','motif29_TAGCTCGGCT','motif30_AGNTCC','motif31_AGNCGT','motif32_TRGNMCTNNT','motif33_AGAGCATGAGACGG','motif34_GANCCT','motif35_CGCCYAGA','motif36_AAGGAGRAN','motif37_GCTCGCA','motif38_TCGNCA','motif39_CCAAGT','motif40_ATGCGGAGGAG','motif41_TSACAA','motif42_CGNTCA','motif43_CCCWGT','motif44_TGAAGST','motif45_GCTCNGG','motif46_CGNAGT','motif47_CGAGTN','motif48_CANTCG','motif49_ACAGRG','motif50_GTCCNA','motif51_CGGNTA','motif52_CGNATG','motif53_ANGCTG','motif54_CGNGTA','motif55_CGTTATAGCC','motif56_GANCGT','motif57_AGGCAT','motif58_CGGNAT','motif59_NCWCCARNR','motif60_GCGNAT','motif61_KAYMGMTN','motif62_CGNGAT','motif63_GTNCCA','motif64_AGTCGN','motif65_TNGCGA','motif66_ACCGRTCA','motif67_GNTAAC','motif68_CTTTTAAAC','motif69_RYKNAAATC','motif70_MAATCGC','motif71_CTCCGCW','motif72_CAGAAMC','motif73_GAGCKMGC','motif74_TTKAAAY','motif75_AGCCGAGCGCT','motif76_GGAGCAGCCAAT','motif77_TCCTTGG','motif78_NCGNWGCAWN','motif79_ACATCTACAA','motif80_CTCTGAGAGAA','motif81_NGCAGAA','motif82_TTGAATCGCGG','motif83_TTWTAAA','motif84_GGKTTYT','motif85_TWNNGCSNA','motif86_CGCACAGACCGCGC','motif87_RCGCACWS','motif88_CCCTCTTT','motif89_CGCCGTGTTTA','motif90_TTATATCGC','motif91_TTCTTTCG','motif92_GCGKWWNAA','motif93_TANTMTCTRWAT','motif94_CATYTSA','motif95_AGCGAGCTAGC','motif96_TKNTTCTGTCTN','motif97_TTCCCT','motif98_GCCGAAGATT','motif99_GYGTSANACG','motif100_GCYTNCTC','motif101_NAGCAASA','motif102_GCAAMGT','motif103_CGGCTAWWT','motif104_GTWSGMT','motif105_KTNGNAGWMG','motif106_KCGCANTC','motif107_CGTCTGCGTA','motif108_AACKSARM','motif109_TCNMTMGC','motif110_AGTCGCAGCG','motif111_WWAATYCGCTCC','motif112_CGYGYAWT','motif113_YGAGCTRTG','motif114_AAACCCGCTC','motif115_CATCAACTAC','motif116_CCAARA','motif117_SKSNGCGCTSN','motif118_AATCCGGCT','motif119_TCAAAANCG','motif120_TTSMTGNNGKTG','motif121_TGCAWTGTA','motif122_TACAAYGGM','motif123_TTGATGCAGTGA','motif124_AATNCANCACT','motif125_TTTAACTCGT','motif126_AATGCAGTCG','motif127_TTTTTACCCTC','motif128_NNGNATRCGWN','motif129_CTCGTAATCT','motif130_TTTCAAACNCCC','motif131_CTGCTTAAATA','motif132_TCRCCAGWY','motif133_TWTAWAGTWGRAG','motif134_ATAAGAGAGGC','motif135_TNKYTGCAKA','motif136_GTCTGCGTCTCT','motif137_MAACAGAAGY','motif138_CTTTWANNYCC','motif139_CGTTCGAATT','motif140_WTAAATAACG','motif141_TTAAACGGC','motif142_TCATATAGAGAAGC','motif143_ATGATGTG','motif144_AAKCMSGT','motif145_GMAGWCGMAW','motif146_AGACGAAGA','motif147_ATATCCAGTG','motif148_NTCSYSTYT','motif149_CAAGCTGTACA','motif150_AGCACAGGCG','motif151_GCCYGTGCMKCW','motif152_GCKYRMKCGS','motif153_ACTYNYYATYG','motif154_GRWGGCAARCG','motif155_AATARSTCCC','motif156_ACTGTAGGACMT','motif157_AAACTWACC','motif158_SRCGWYACA','motif159_ACACATACTACA','motif160_AGCCGGTAACG','motif161_CGGCTTGATT','motif162_AGTTACCGTCA','motif163_GARTCGCCCTGTNA','motif164_AGCCGATTTG','motif165_AAAGTTACTG','motif166_TAMAACTTTGS','motif167_TTGGGTAGGAG','motif168_TCTCAGAGTATAAA','motif169_GCCTGGCC'];
var pval = [</html>{{{tfbs_overrepresentation_for_novel_motifs}}}<html>];
var data = [];
for(i1=0;i1<motifs.length;i1++){
data.push([motifs[i1],pval[i1]]);
}
 
var tfbs_overexpression_table = $('#tfbs_overexpression_table').dataTable({
"sScrollY": "300px",
                "bScrollCollapse": true,
"bPaginate": true,
"bFilter": true,
"bInfo": true,
                "iDisplayLength": 10,
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
"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)", "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_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"} ]});
 
$('#tfbs_overexpression_table_export_tool').before(tfbs_overexpression_table_tools.dom.container );
 
var tfbs_overexpression_jaspar_table= $('#tfbs_overexpression_jaspar').dataTable({
"sScrollY": "300px",
"sScrollY": "300px",
                 "bScrollCollapse": true,
                 "bScrollCollapse": true,
Line 47: Line 170:
                 "iDisplayLength": 10,
                 "iDisplayLength": 10,
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
"aaSorting": [[0,'asc']],
"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) {                   
"aoColumnDefs": [ { "sType": "numeric", "aTargets": [2] }]
                  var num =obj.aData[obj.iDataColumn];
                  var num_as_number=Number(num);
                  return num_as_number.toFixed(2) ;
} }],
"aaSorting": [[ 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"} ]});


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"} ]});
$('#tfbs_overexpression_jaspar_table_export_tool').before(tfbs_overexpression_jaspar_table_tools.dom.container );
// tfbs results table end


$('#gostat_table_export_tool').before( oTableTools.dom.container );
// tf chipseq results table start
// GOstat results table end
var tfbs_chipseq_enrich_table=$('#tf_chipseq_enrich').dataTable({
"sScrollY": "300px",
                "bScrollCollapse": true,
"bPaginate": true,
"bFilter": true,
"bInfo": true,
                "iDisplayLength": 10,
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
"aaSorting": [[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) {                   
                  var num =obj.aData[obj.iDataColumn];               
                  return exp_converter(num,2,"e") ;
} },{  "sType": "numeric", "aTargets": [3],"fnRender": function (obj) {                   
                  var num =obj.aData[obj.iDataColumn];
                    return exp_converter(num,2,"e") ;
} },{"sType": "numeric", "aTargets": [4],"fnRender": function (obj) {                   
                  var num =obj.aData[obj.iDataColumn];             
                  return exp_converter(num,2,"e") ;
}}]
});
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>


Full id: [[full_id::{{{full_id}}}]]
Full id: [[full_id::{{{full_id}}}]]
Line 69: Line 221:


== Phase1 CAGE Peaks ==
== Phase1 CAGE Peaks ==
{{#ask:[[Category:FFCP]][[Species::Human (Homo sapiens)]][[Coexpression_cluster_id::{{PAGENAME}}]]|?Short_description|format=ttable|class=ffcp_list|limit=20000}}
<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}}
<br>
<br>
== Pathway enrichment analysis  ==
 
{{#info:Analyst: Emmanuel Dimont
{{Fontsize|3|Enriched pathways on this co-expression cluster}}{{#info:<b>Summary:</b>
<br>Integrating CAGE clusters and expression array data is combined at the functional level, resulting in
<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
defining common informative pathways and expression analysis results for pathway lists.
<br>
<br>
<br>link to the source data.
<br>link to source dataset
<br>[http://fantom.gsc.riken.jp/5/datafiles/sstar/Co-expression/pathway_enrichment/hg19/{{{full_id}}}.txt data]
<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_modules.tar.gz data]
}}
}}
{{#if: {{#pos:{{{pathway_enrichment}}}|;}} |
----
<html>
{{#if:{{{pathway_enrichment}}}|<span id="pathway_enrichment_table_export_tool"></span>
<script type="text/javascript">
<table class="pathway_enrichment"><html><thead></html>
$(document).ready(function() {
<tr><th>p.value</th><th>FDR</th><th>nGenes</th><th>nPathway</th><th>Name</th></tr>
    $('.pathway_enrichment').dataTable({
<html></thead><tbody></html>
"sScrollY": "300px",
                "bScrollCollapse": true,
"bPaginate": true,
"bFilter": true,
"bInfo": true,
                "iDisplayLength": 10,
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
"aaSorting": [[0,'asc']],
"aoColumnDefs": [{"fnRender": function ( o, val ) {
var name = o.aData[4].split(":");
if(name[0].indexOf("KEGG") != -1){
return "<a href=\"http://www.genome.jp/dbget-bin/www_bget?pathway:map"+name[1]+"\">"+name[0]+"</a>";
}else if(name[0].indexOf("Wikipathways") != -1){
return "<a href=\"http://www.wikipathways.org/index.php/Pathway:"+name[1]+"\">"+name[0]+"</a>";
}else if(name[0].indexOf("Reactome") != -1){
return "<a href=\"http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID="+name[1]+"\">"+name[0]+"</a>";
}else if(name[0].indexOf("Netpath") != -1){
return "<a href=\"http://www.netpath.org/pathways?path_id="+name[1]+"\">"+name[0]+"</a>";
}else if(name[0].indexOf("Static Module") != -1){
return "<a href=\"http://genomebiology.com/content/11/5/R53\">"+name[0]+"</a>";
}else{
return name[0];
}
}, "aTargets": [ 4 ]}, { "sType": "numeric", "aTargets": [0,1] }]
});
});
</script>
</html>
<table class="pathway_enrichment"><html><thead></html><tr><th>p.value</th><th>FDR</th><th>nGenes</th><th>nPathway</th><th>Name</th></tr><html></thead><tbody></html>
{{#arraymap:{{{pathway_enrichment}}}|!|$
{{#arraymap:{{{pathway_enrichment}}}|!|$
|<tr><td>{{#replace:$|;|</td><td>}}</td></tr>
|<tr><td>{{#replace:$|;|</td><td>}}</td></tr>
|}}
|}}
<html></tbody></html></table>
<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/hg19_co-expression_GOstats.tar.gz  data]
}}
}}
<br>
----
 
{{#switch:{{#show:{{FULLPAGENAME}}|?species}}
== GOStat results on Coexpression cluster  ==
|Human (Homo sapiens)=
{{#info:The results for GOStat analysis on co-expressed clusters("All" category).  <br>Analyst: Erik Arner}}
{{#ifeq:{{#sub:{{{gostat_on_coexpression_clusters}}}|0|2}}|GO|<span id="gostat_table_export_tool"></span>
{{#if:{{{gostat_on_MCL_coexpression}}}|
<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"><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>
Line 131: Line 257:
}}
}}
</tr>
</tr>
<html></tbody></html></table>
<html></tbody></html></table>|No GOStat results}}
|no results for this coexpression
|Mouse (Mus musculus)=
{{#ifeq:{{#sub:{{{gostat_on_MCL_coexpression}}}|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>
<tr>
{{#arraymap:{{{gostat_on_MCL_coexpression}}}|$|$
|<td>[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term={{#explode:$|!|0}} {{#explode:$|!|0}}]</td><td>{{#explode:$|!|1}}</td><td>{{#explode:$|!|2}}</td>
|</tr><tr>
}}
</tr>
<html></tbody></html></table>|No GOStat results}}
|No results for this coexpression
}}
}}
<br>
<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
{{#if: {{#pos:{{{gostat_on_coexpression_clusters}}}|GO}} |
<br><br>links to source dataset<br><br>
<table class="wikitable mw-collapsible" style="float:left;"><tr><th scope="col"></th></tr><tr><td>
{{#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>
<div style="height:300px; overflow-y:scroll; resize:both;">
{{#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>
{{#motif_gotable:{{{gostat_on_coexpression_clusters}}}}}
{{#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>
</div></td></tr></table>
}}
}}
<div style="clear:both;"></div>
----
-->
<br>
== Sample ontology enrichment analysis ==
{{#info:The results for enrichment analysis on the data of MCL co-expression cluster.  That are sorted by ontologies each samples belonging. <br>Analyst: Hideya Kawaji}}
{{#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 id="enrichment_list_cl"><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_hg19_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 id="enrichment_list_uberon"><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}}}|;|$
|{{#ifexist:{{#explode:$|!|0}}|<tr><td>[[{{#explode:$|!|0}}|{{#show:{{#explode:$|!|0}}|?name}}]]</td><td>{{#explode:$|!|1}}</td><td>{{#explode:$|!|2}}</td></tr>| }}
|<!--{{#set:MCL_coexpression_hg19_ontology_enrichment_uberon={{#replace:$|!|;}}}}-->[[{{#explode:$|!|0}}|{{#show:{{#explode:$|!|0}}|?name}}]]</td><td>{{#explode:$|!|1}}</td><td>{{#explode:$|!|2}}
|}}
|</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 id="enrichment_list_doid"><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}}}|;|$
|{{#ifexist:{{#explode:$|!|0}}|<tr><td>[[{{#explode:$|!|0}}|{{#show:{{#explode:$|!|0}}|?name}}]]</td><td>{{#explode:$|!|1}}</td><td>{{#explode:$|!|2}}</td></tr>| }}
|<!--{{#set:MCL_coexpression_hg19_ontology_enrichment_disease={{#replace:$|!|;}}}}-->[[{{#explode:$|!|0}}|{{#show:{{#explode:$|!|0}}|?name}}]]</td><td>{{#explode:$|!|1}}</td><td>{{#explode:$|!|2}}
|}}
|</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>
== TFBS overrepresentation ==
{{#info: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. <br>Analyst: Michiel de Hoon}}
<html>
<script type="text/javascript">
$(document).ready(function() {
var motifs = ['motif1_TCGNAG','motif2_GCTGGAGG','motif3_CGCTNA','motif4_TGTCTA','motif5_CAGTGT','motif6_AAGACT','motif7_CGNATC','motif8_CCATGN','motif9_ANGGCT','motif10_SCGGAGASN','motif11_GCGANT','motif12_ACTAAG','motif13_GAGGATGCK','motif14_TCNACG','motif15_ACTGTG','motif16_ACCAG','motif17_CGCTAN','motif18_CATCAG','motif19_GYTGGMC','motif20_TGNAGC','motif21_TCTTGA','motif22_GGMCTG','motif23_CGCNAT','motif24_AGAACT','motif25_GATCCN','motif26_CTCCGCAGTA','motif27_CCTGCA','motif28_CGTNCA','motif29_TAGCTCGGCT','motif30_AGNTCC','motif31_AGNCGT','motif32_TRGNMCTNNT','motif33_AGAGCATGAGACGG','motif34_GANCCT','motif35_CGCCYAGA','motif36_AAGGAGRAN','motif37_GCTCGCA','motif38_TCGNCA','motif39_CCAAGT','motif40_ATGCGGAGGAG','motif41_TSACAA','motif42_CGNTCA','motif43_CCCWGT','motif44_TGAAGST','motif45_GCTCNGG','motif46_CGNAGT','motif47_CGAGTN','motif48_CANTCG','motif49_ACAGRG','motif50_GTCCNA','motif51_CGGNTA','motif52_CGNATG','motif53_ANGCTG','motif54_CGNGTA','motif55_CGTTATAGCC','motif56_GANCGT','motif57_AGGCAT','motif58_CGGNAT','motif59_NCWCCARNR','motif60_GCGNAT','motif61_KAYMGMTN','motif62_CGNGAT','motif63_GTNCCA','motif64_AGTCGN','motif65_TNGCGA','motif66_ACCGRTCA','motif67_GNTAAC','motif68_CTTTTAAAC','motif69_RYKNAAATC','motif70_MAATCGC','motif71_CTCCGCW','motif72_CAGAAMC','motif73_GAGCKMGC','motif74_TTKAAAY','motif75_AGCCGAGCGCT','motif76_GGAGCAGCCAAT','motif77_TCCTTGG','motif78_NCGNWGCAWN','motif79_ACATCTACAA','motif80_CTCTGAGAGAA','motif81_NGCAGAA','motif82_TTGAATCGCGG','motif83_TTWTAAA','motif84_GGKTTYT','motif85_TWNNGCSNA','motif86_CGCACAGACCGCGC','motif87_RCGCACWS','motif88_CCCTCTTT','motif89_CGCCGTGTTTA','motif90_TTATATCGC','motif91_TTCTTTCG','motif92_GCGKWWNAA','motif93_TANTMTCTRWAT','motif94_CATYTSA','motif95_AGCGAGCTAGC','motif96_TKNTTCTGTCTN','motif97_TTCCCT','motif98_GCCGAAGATT','motif99_GYGTSANACG','motif100_GCYTNCTC','motif101_NAGCAASA','motif102_GCAAMGT','motif103_CGGCTAWWT','motif104_GTWSGMT','motif105_KTNGNAGWMG','motif106_KCGCANTC','motif107_CGTCTGCGTA','motif108_AACKSARM','motif109_TCNMTMGC','motif110_AGTCGCAGCG','motif111_WWAATYCGCTCC','motif112_CGYGYAWT','motif113_YGAGCTRTG','motif114_AAACCCGCTC','motif115_CATCAACTAC','motif116_CCAARA','motif117_SKSNGCGCTSN','motif118_AATCCGGCT','motif119_TCAAAANCG','motif120_TTSMTGNNGKTG','motif121_TGCAWTGTA','motif122_TACAAYGGM','motif123_TTGATGCAGTGA','motif124_AATNCANCACT','motif125_TTTAACTCGT','motif126_AATGCAGTCG','motif127_TTTTTACCCTC','motif128_NNGNATRCGWN','motif129_CTCGTAATCT','motif130_TTTCAAACNCCC','motif131_CTGCTTAAATA','motif132_TCRCCAGWY','motif133_TWTAWAGTWGRAG','motif134_ATAAGAGAGGC','motif135_TNKYTGCAKA','motif136_GTCTGCGTCTCT','motif137_MAACAGAAGY','motif138_CTTTWANNYCC','motif139_CGTTCGAATT','motif140_WTAAATAACG','motif141_TTAAACGGC','motif142_TCATATAGAGAAGC','motif143_ATGATGTG','motif144_AAKCMSGT','motif145_GMAGWCGMAW','motif146_AGACGAAGA','motif147_ATATCCAGTG','motif148_NTCSYSTYT','motif149_CAAGCTGTACA','motif150_AGCACAGGCG','motif151_GCCYGTGCMKCW','motif152_GCKYRMKCGS','motif153_ACTYNYYATYG','motif154_GRWGGCAARCG','motif155_AATARSTCCC','motif156_ACTGTAGGACMT','motif157_AAACTWACC','motif158_SRCGWYACA','motif159_ACACATACTACA','motif160_AGCCGGTAACG','motif161_CGGCTTGATT','motif162_AGTTACCGTCA','motif163_GARTCGCCCTGTNA','motif164_AGCCGATTTG','motif165_AAAGTTACTG','motif166_TAMAACTTTGS','motif167_TTGGGTAGGAG','motif168_TCTCAGAGTATAAA','motif169_GCCTGGCC'];
var pval = [</html>{{{tfbs_overrepresentation_for_novel_motifs}}}<html>];
var data = [];
for(i1=0;i1<motifs.length;i1++){
data.push([motifs[i1],pval[i1]]);
}
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{{#ifeq:{{#show:{{FULLPAGENAME}}|?species}}
});
|Human (Homo sapiens)
</script>
|{{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>
</html><br>
link to source data <br> Novel motifs <br>
=== Novel motifs ===
[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19.novel_motif.coexpression_clusters_overrepresentation.txt.gz data] <br>
<table id="tfbs_overexpression_table"></table><br>
<br> Jaspar motifs <br>
=== JASPAR motifs ===
[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz data]
<table id="tfbs_overexpression_jaspar"><html><thead></html>
}}
----
{{Fontsize|3|Novel motifs}}{{#if:{{{tfbs_overrepresentation_for_novel_motifs}}}
|<span id="tfbs_overexpression_table_export_tool"></span><table id="tfbs_overexpression_table"></table>
|No results for this section
}} <br><br>
{{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>
<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 234: Line 331:
<html></tbody></html>
<html></tbody></html>
</table>
</table>
<br><br>
|No results for this section
== ENCODE TF ChIP-seq peak enrichment analysis ==
}}
{{#info: Method: 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>Analyst: Erick Arner}}
|
}} <br><br>


{{#if: {{#pos:{{{tf_chipseq_enrich}}}|;}} |
{{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
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)  
<br><br>link to source dataset<br>
<html>
<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]
<script type="text/javascript">
}}
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----
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</html>
<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"><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}}}|!|$
Line 264: Line 350:
|No analysis results for this cluster
|No analysis results for this cluster
}}
}}
<br>
<br>
== Relative expression of the co-expression cluster ==
<br>
{{#info: <br>Analyst: }}
{{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]}}
{{#ifexpr:{{#sub:{{{id}}}|1}} < 306|
----
<html>
{{#ifexpr:{{#sub:{{{id}}}|1}} < 306|<html><script type="text/javascript">
<script type="text/javascript">
$(document).ready(function() {
$(document).ready(function() {
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Line 280: Line 364:
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<table id="coexpression_dpi_cluster_scores_median_table"></table>
<table id="coexpression_dpi_cluster_scores_median_table"></table>
</html>
</html>
Line 308: Line 395:
|{{{coexpression_dpi_cluster_scores_median}}}
|{{{coexpression_dpi_cluster_scores_median}}}
}}
}}
|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 10:13, 8 April 2014


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

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

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 "{".

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