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Full id: [[full_id::{{{full_id}}}]]
{{Loading|loadingimage=sprites.gif}}<html>
{{#set:id={{{id}}}}}
<script type="text/javascript" src="/5/sstar/jquery-1.7.1.min.js"></script>
{{#set:cp_member_count={{#ask:[[Category:FFCP]][[Coexpression_cluster_id::{{{id}}}]]|format=count}}}}
<script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.min.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">
@import "/5/sstar/rb_js/html5button/datatables.css";
@import "/5/sstar/rb_js/datatables/extras/TableTools/media/css/TableTools.css";


== Phase1 CAGE Peaks ==
.table_title{
 
text-align:left;
<html>
font-size:small;
<style type="text/css" title="currentStyle">
color:darkgoldenrod;
@import "/resource_browser/rb_js/datatables/media/css/jquery.dataTables.css";
}
</style>
</style>
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.js"></script>
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/sparkline/jquery.sparkline.min.js"></script>
<script type="text/javascript" charset="utf-8">
 
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() {
$('#ffcp_list').html( '<table cellpadding="0" cellspacing="0" border="0" class="display" id="ffcp_list_cont"></table>' );
$('#ffcp_list_cont').dataTable( {
"bAutoWidth": false,
"iDisplayLength": 25,
//"aLengthMenu": [[25, 100, 500, -1], [25, 100, 500, "All"]],
"aaData": aDataSet,
"aoColumns": [
{ "sTitle": "CAGE Peak ID",
"fnRender": function(obj) {
var id = obj.aData[ obj.iDataColumn ];
return sReturn = "<a href=\"/resource_browser/index.php/FFCP PHASE1:Hg19::"+id+"\">"+id+"</a>";
}
},
{ "sTitle": "Short description","sWidth": "60%"},
//{ "sTitle": "Species","sWidth": "30%","sClass": "micro_chart"},


]
} );
//$('.micro_chart').sparkline('html',{width:200});
} );
</script>
<div id="ffcp_list"></div>
</html>
<br>
== Pathway enrichment analysis  ==
{{#info:Analyst: Emmanuel Dimont}}
{{#if: {{#pos:{{{pathway_enrichment}}}|;}} |
<html>
<script type="text/javascript">
<script type="text/javascript">
$(document).ready(function() {
$(document).ready(function() {
    $('.pathway_enrichment').dataTable({
// FFCP list start
"sScrollY": "300px",
var ffcp_list_table = $('.ffcp_list').DataTable({
"bPaginate": false,
    dom: 'Blfrtip',
"bScrollCollapse": true,
    lengthMenu: [[10, 25, 50, -1], [10, 25, 50, "All"]],
"iDisplayLength": -1,
    buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
"aaSorting": [[0,'asc']],
    columns: [{title:"Id"},{title:"Short description"}]
"aoColumnDefs": [{"fnRender": function ( o, val ) {
});
var name = o.aData[4].split(":");
// FFCP list end
if(name[0].indexOf("KEGG") != -1){
if($('.pathway_enrichment').size()>0) {
// Pathway enrichment analysis start
var pathway_enrichment_table =$('.pathway_enrichment').DataTable({
        dom: 'Blfrtip',
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
scrollY: "300px",
        scrollCollapse: true,
        pageLength: 10,
        lengthMenu: [[10, 50, -1], [10, 50, "All"]],
order: [[1,'asc']],
columnDefs: [{render: function ( data, type, row, meta ) {
var name = data.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>";
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] }]
}, targets: [ 4 ]}, { type: "numeric", targets: [0,1], render: function ( data, type, row, meta ) {
                  var num =data;
                  return exp_converter(num,2,"e");
} }]
});
 
}
 
// 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({
        dom: 'lfrtip',
        scrollY: "300px",
        scrollCollapse: true,
        pageLength: 10,
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
order: [[0,'asc']],
columnDefs: [{type: "numeric", targets: [2],
        render: function ( data, type, row, meta ) {
                  var num =data;             
                  return exp_converter(num,2,"e");
} }]
});
}
// GOstat results table end
 
// sample ontology enrichment list start
var enrichment_list_cl_table = $('#enrichment_list_cl').DataTable({
        dom: 'lfrti',
scrollY: "300px",
        scrollCollapse: true,
        pageLength: -1,
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
columnDefs: [{ orderable: false, targets: [ 0 ] },  { type: "numeric", targets: [1] }, { width: "50pt", targets: [ 1 ] }],
order: [[ 1, "asc" ]]
});
});
var enrichment_list_uberon_table = $('#enrichment_list_uberon').DataTable({
        dom: 'lfrti',
scrollY: "300px",
        scrollCollapse: true,
        pageLength: -1,
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
columnDefs: [{ orderable: false, targets: [ 0 ] },  { type: "numeric", targets: [1] }, { width: "50pt", targets: [ 1 ] }],
order: [[ 1, "asc" ]]
});
});
</script>
</html>
<table class="pathway_enrichment"><html><thead></html><tr><th>p.value</th><th>FDR</th><th>nGenes</th><th>nPathway</th><th>Name</th></tr><html></thead><tbody></html>
{{#arraymap:{{{pathway_enrichment}}}|!|$
|<tr><td>{{#replace:$|;|</td><td>}}</td></tr>
|}}
<html></tbody></html></table>
}}


<!--
== KEGG pathway enrichment analysis  ==
{{#info:The strongest KEGG pathway enrichments  <br>Analyst: }}
{{#if: {{#pos:{{{kegg_enrichment}}}|;}} |
<table class="wikitable sortable"><tr><th>KEGG id</th><th>Pathway name</th><th>P-value</th></tr>
{{#arraymap:{{{kegg_enrichment}}}|!|$
|{{#set:kegg_enrichment=$}}<tr><td>{{#replace:$|;|</td><td>}}</td></tr>
|}}
</table>
}}
-->


== GOStat results on Coexpression cluster  ==
{{#info:The results for GOStat analysis on co-expressed clusters("All" category).  <br>Analyst: Erik Arner}}
{{#if: {{#pos:{{{gostat_on_coexpression_clusters}}}|GO}} |
<table class="wikitable mw-collapsible" style="float:left;"><tr><th scope="col"></th></tr><tr><td>
<div style="height:300px; overflow-y:scroll; resize:both;">
{{#motif_gotable:{{{gostat_on_coexpression_clusters}}}}}
</div></td></tr></table>
}}


<div style="clear:both;"></div>


== Sample enrichment analysis  ==
var enrichment_list_disease_table= $('#enrichment_list_doid').DataTable({
{{#info:The results for enrichment analysis on "All" data of MCL co-expression cluster. That are sorted by ontologies each samples belonging. [https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v6_ontology_term_enrichment_on_MCL_coexp_cluster_120516/ Original Data]  <br>Analyst: Hideya Kawaji}}
        dom: 'lfrti',
{{#if: {{#pos:{{{ontology_enrichment_celltype}}}|CL}} |
scrollY: "300px",
<table class="wikitable mw-collapsible" style="float:left;"><tr><th scope="col">Cell Type (CL)</th></tr><tr><td>
        scrollCollapse: true,
<div style="height:300px; overflow-y:scroll; resize:both;">
        pageLength: -1,
{{#ffcp_ontology_enrichtable:{{{ontology_enrichment_celltype}}}}}
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
</div></td></tr></table>
columnDefs: [{ orderable: false, targets: [ 0 ] },  { type: "numeric", targets: [1] }, { width: "50pt", targets: [ 1 ] }],
}}
order: [[ 1, "asc" ]]
{{#if: {{#pos:{{{ontology_enrichment_disease}}}|DOID}} |
});
<table class="wikitable mw-collapsible" style="float:left;"><tr><th scope="col">Human Disease (DOID)</th></tr><tr><td>
 
<div style="height:300px; overflow-y:scroll; resize:both;">
 
{{#ffcp_ontology_enrichtable:{{{ontology_enrichment_disease}}}}}
// sample ontology enrichment list end
</div></td></tr></table>
}}
{{#if: {{#pos:{{{ontology_enrichment_uberon}}}|UBERON}} |
<table class="wikitable mw-collapsible" style="float:left;"><tr><th scope="col">Uber Anatomy (UBERON)</th></tr><tr><td>
<div style="height:300px; overflow-y:scroll; resize:both;">
{{#ffcp_ontology_enrichtable:{{{ontology_enrichment_uberon}}}}}
</div></td></tr></table>
}}
<div style="clear:both;"></div>


== TFBS overrepresentation ==
// tfbs results table start
{{#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}}
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'];
<html>
var pval = [</html>{{{tfbs_overrepresentation_for_novel_motifs}}}<html>];
<script type="text/javascript">
$(document).ready(function() {
var motifs = ['1-CAATGACATC','1-CSGATGAAT','1-GGAGGAGRAGG','1-TATKWNTTCMGTGTY','1-TGAGTCATTTCCT','1-TGGTCCYSCTGGTCC','1-TWTTWVNSCS','10-ACTTCCTCTTCC','10-ATCGATTG','10-CGCGTGTTA','10-GCTTHCTCAT','10-GGGAAGTGACG','10-GGTTTCTTTT','10-GTAACHDC','10-GTGATGTCACT','10-GTTTCTACG','10-TCCTCCGATT','10-TCTATGAC','10-TCTBACKA','10-TGCGTCATTT','10-TGTCACTGCG','10-VGGAAACGAC','10-WGACAAC','10-YGAGTCHYTD','11-AACGAATCGA','11-AGGCAGTACCTC','11-CGGGGAAATTAC','11-CGTCTGCGTA','11-GATTTCACAACC','11-GCTGTGACGA','11-GTAACGCCCC','11-TCGGGGTGTTTT','11-TSACGCSTCAGT','11-TTTGAGGAAGTTG','11-WACGYACGTG','11-WGTGKKTTTT','12-CGCGGCGGCGGCT','12-CSCCYTTTWA','12-GCNGTGTRAC','12-GTAGCWCSGC','12-GWTYKNKNTTG','12-GYTTGWTATTG','12-SSARTSACMRCA','12-TGCAGTNTTT','12-TGWCACGGCG','13-AATTCCG','13-CBTACGCAA','13-CGTCACAGGAAAC','13-GGATTTGT','13-GGCTGKTACT','13-GTACTTTCCA','13-GTGTCABACG','13-MGCTGACACACGC','13-STTYSWCWTCY','14-ACWTCYTGCTT','14-ATTACGC','14-CACTTCCGTAA','14-RSCGSWVTCT','14-TACGCCC','14-TSTCRGCTR','14-TTAMCGKAA','15-AGRMAACCG','15-CWTCTGACTV','15-NNNTDAGHAA','15-TKABWMGC','16-ATGACTCACTT','16-GCTTYCTS','16-GTKACGDWGC','16-RBYKBTWACG','16-TCAGCTGACG','18-GAAGTGGGTGG','2-AATGCGTT','2-AWTSGCT','2-CCTTTTAA','2-CGBTDATTA','2-GATYGSAS','2-SVGTTTAAA','2-TATATAGCCG','2-TTCAAATCTCCCGC','2-TTWAACCS','3-AAACYGGTTTG','3-AGAAAAVGGAACT','3-ATAAADCGC','3-AWTTSSYS','3-CCCCCCTTTTTT','3-CGCCCATT','3-CGCTATTTAAAC','3-GATGATGAT','3-GCGGGAGGGAGT','3-GCGTTTGAAT','3-MASTTCCCCTTW','3-TTTCGAAT','4-AAAACGCGC','4-AAAWRCG','4-CGGAGAGATA','4-CGTRGTTT','4-CTCTCTCTC','4-GAAGTRCCCAAGAAA','4-GCAAATCGGA','4-GCYTCTYTBTTTTT','4-GGGTTAAA','4-HCTTHYBCTD','4-NTGTTTTTTTKTC','4-SGSTTAWA','4-TAAAAAGACAGC','4-TTAAACCG','4-TTTAAAGCGG','4-TTYCTCTKCWGMR','5-ATTGGGCGG','5-AWTKGKCGVG','5-CCCGCCTTTA','5-CCGGATTTA','5-CGGGAAACTAC','5-CGRAWAT','5-CGTCACTMGT','5-CGTCTGATA','5-GCGAATA','5-GCGATTCAAA','5-GCTTSYTGTTTW','5-GGTGRTTDTT','5-GTTGTTGC','5-NCTSTCTCTTTN','5-SBGTYRTYWGRS','5-TCATTTGC','5-TCTGCGTCAC','5-TGWTTKCCWG','5-TTAATCAGCC','5-WCCGWTAR','6-AAAAACGCCC','6-AAGTTCCGC','6-AATCTCGC','6-AATTAGAGCG','6-ACGCTTGTTT','6-AGGAAGTGAYGYAA','6-AGTTCTGTTTT','6-ATATTTGGCA','6-ATGATTAGTCA','6-ATTAAAGGCG','6-CGCCTAAA','6-CGHYWRA','6-CGTTTCA','6-CTGATYACA','6-CTTCCTGTCAGAG','6-CTTGTGA','6-GAGAGGGGGTGG','6-GCGGTTTTTT','6-GCTGCAAATAGA','6-GTTAACCAATC','6-HNCGKHTKWGRA','6-HWDHHWNCASC','6-TCGGCTG','6-TDTAAWSAG','6-TTACAGC','6-TTAHWHCG','6-YWARCGCN','7-AAAAGMGCS','7-AGTCATATGAC','7-AVAVAGSAAAST','7-CGTCTGA','7-CGTTGCTA','7-GCAGAYTK','7-GCAKYWTTTWT','7-GCTGCATT','7-GCWGCATT','7-GTGTGTGTGT','7-GTKTGWCWC','7-SCGYTTAA','7-TGTTTCT','7-TSTCWCG','7-TTTYTTTTTTCTG','8-AGCAGAAGTG','8-ATCCRAGC','8-CACACYCMCACA','8-CATACGC','8-CGGWGAYW','8-GAAACAACCT','8-GAATGAAAGCG','8-GGHAACT','8-GTTGTTKKGKT','8-HTTTGCGC','8-MHRGTVACTTBN','8-SGAAATGACA','8-TAWAARGCG','8-TBTSTGTBTGC','8-TCGGAGT','8-TGCTGATT','8-TTTGCGGAAGC','8-WNHTTDCGTKTYW','9-AAACAACGCC','9-AAACTGCA','9-AATRCATCGC','9-ACTTMCTHC','9-CGGAAACAA','9-CTGTTGCGT','9-CTSASTCACTG','9-GATCCGCTA','9-GCTAGCAAAA','9-GGGGTTT','9-GTAGGAT','9-HGASWSVGYG','9-RTKACAA','9-TAGTTACCG','9-TATAWACGC','9-TATCCGMH','9-TDDCRNMASM','9-TTTCSCT','9-VCTTKCTKC','AAAAGCACTGC,motif961','AAAARAAG,motif736','AAACCCCCCC,motif448','AAACTATA,motif684','AAATAGGGAAGT,motif184','AAGACTACCA,motif544','AAGATCGAS,motif641','AAGCAGGAA,motif523','AATGGGG,motif928','AATTCCCGG,motif577','AAYAATC,motif540','ACGAGACGGATGA,motif936','ACGTCACAA,motif25','AGACTCAGA,motif213','AGAGAAAGAG,motif627','AGCASAGGA,motif488','AGKAGGACCA,motif546','AGTCTCAAGTT,motif953','AGTTTCCGC,motif855','AHR_si','AIRE','AIRE_f2','ALX1','AP2A_f2','ARAGGGGK,motif561','ARI3A_do','ARI5B_f1','AR_LNCAP-AR-ChIP-Seq/Homer','ATAGCGAC,motif639','ATCATTTCC,motif740','ATF5_si','ATF6','ATGATGGTGGC,motif457','ATGGAGGTCGTC,motif943','ATTGGCGGCG,motif630','ATYACCC,motif728','BPTF_si','CAAACTTAGCC,motif480','CAATGATGG,motif925','CACACTTTTTA,motif844','CACGAAG,motif790','CACTTCCTTCCT,motif281','CAGAGTTCTAG,motif792','CARGWTGY,motif333','CATCCATGTC,motif545','CATTAGGACCAG,motif719','CATTRTGACG,motif6','CAYAAST,motif606','CCAATCCGGT,motif823','CCAGTACA,motif794','CCCACAGACTCAG,motif858','CCCCCTATTA,motif248','CCCCCTCTCTCC,motif580','CCCGAAC,motif795','CCCGATCC,motif958','CCGCCAATYC,motif849','CCGTCTYT,motif741','CDC5L_si','CDX1,2,4','CDX2_f1','CEBPB_ThioMac-CEBPb-ChIP-Seq/Homer','CEBPB_f1','CGATCCGGAT,motif767','CGCTCTCKCT,motif771','CGCTTAAA,motif359','CGGAAACGGAA,motif609','CGGCAGCGGA,motif385','CGGCTTAAA,motif768','CGTVTCAYCA,motif126','CKACTAC,motif854','CNhs10624_bl_f0','CNhs10625_bl_f0','CNhs10632_bl_f0','CNhs10633_bl_f0','CNhs10634_bl_f2','CNhs10636_bu_f0','CNhs10643_bu_f2','CNhs10731_bl_f2','CNhs10734_bu_f2','CNhs10751_bu_f2','CNhs10752_bl_f1','CNhs10839_bl_f1','CNhs10843_bu_f2','CNhs10846_bu_f1','CNhs10846_bu_f2','CNhs11047_bu_f2','CNhs11051_bl_f2','CNhs11051_bu_f2','CNhs11068_bl_f2','CNhs11073_bl_f1','CNhs11073_bl_f2','CNhs11185_bl_f2','CNhs11245_bl_f2','CNhs11253_bl_f1','CNhs11257_bl_f2','CNhs11258_bu_f2','CNhs11265_bl_f2','CNhs11267_bl_f2','CNhs11270_bl_f2','CNhs11276_bl_f2','CNhs11279_bu_f2','CNhs11284_bl_f2','CNhs11287_bu_f1','CNhs11290_bl_f2','CNhs11331_bl_f2','CNhs11332_bl_f1','CNhs11341_bu_f1','CNhs11344_bl_f2','CNhs11354_bl_f2','CNhs11372_bl_f2','CNhs11377_bl_f2','CNhs11380_bl_f1','CNhs11380_bu_f0','CNhs11716_bu_f2','CNhs11725_bl_f1','CNhs11725_bu_f2','CNhs11729_bl_f2','CNhs11741_bu_f1','CNhs11747_bu_f2','CNhs11750_bl_f0','CNhs11756_bl_f2','CNhs11756_bu_f1','CNhs11774_bu_f2','CNhs11777_bu_f2','CNhs11781_bl_f0','CNhs11781_bu_f1','CNhs11786_bl_f2','CNhs11786_bu_f1','CNhs11789_bl_f2','CNhs11793_bu_f1','CNhs11811_bl_f2','CNhs11822_bl_f1','CNhs11822_bl_f2','CNhs11828_bl_f2','CNhs11828_bu_f0','CNhs11828_bu_f1','CNhs11828_bu_f2','CNhs11833_bl_f2','CNhs11840_bl_f0','CNhs11840_bl_f2','CNhs11842_bl_f0','CNhs11848_bu_f2','CNhs11853_bu_f1','CNhs11862_bl_f2','CNhs11882_bl_f2','CNhs11882_bu_f2','CNhs11892_bl_f2','CNhs11893_bl_f1','CNhs11893_bu_f2','CNhs11931_bu_f2','CNhs11986_bl_f2','CNhs11986_bu_f1','CNhs11990_bl_f1','CNhs11990_bl_f2','CNhs12001_bu_f0','CNhs12008_bl_f1','CNhs12008_bu_f2','CNhs12013_bu_f2','CNhs12028_bl_f2','CNhs12030_bl_f0','CNhs12035_bu_f0','CNhs12036_bu_f2','CNhs12040_bu_f2','CNhs12043_bu_f1','CNhs12065_bl_f2','CNhs12087_bl_f0','CNhs12087_bu_f1','CNhs12092_bu_f2','CNhs12093_bu_f2','CNhs12096_bl_f2','CNhs12098_bu_f2','CNhs12102_bl_f1','CNhs12103_bl_f1','CNhs12105_bl_f2','CNhs12128_bu_f2','CNhs12192_bu_f0','CNhs12316_bu_f2','CNhs12323_bu_f0','CNhs12341_bl_f2','CNhs12345_bu_f2','CNhs12348_bl_f1','CNhs12494_bl_f0','CNhs12494_bu_f1','CNhs12497_bu_f2','CNhs12498_bl_f2','CNhs12500_bl_f2','CNhs12500_bu_f2','CNhs12502_bl_f1','CNhs12518_bu_f0','CNhs12522_bl_f0','CNhs12523_bl_f1','CNhs12524_bu_f2','CNhs12525_bl_f0','CNhs12530_bu_f2','CNhs12545_bl_f2','CNhs12546_bu_f2','CNhs12566_bl_f1','CNhs12574_bl_f1','CNhs12622_bl_f1','CNhs12623_bl_f2','CNhs12623_bu_f2','CNhs12625_bl_f1','CNhs12625_bu_f2','CNhs12626_bu_f0','CNhs12626_bu_f2','CNhs12627_bu_f2','CNhs12703_bl_f2','CNhs12727_bl_f1','CNhs12733_bl_f2','CNhs12825_bl_f2','CNhs12838_bl_f1','CNhs12839_bu_f2','CNhs12846_bl_f1','CNhs12846_bl_f2','CNhs12849_bu_f0','CNhs12849_bu_f1','CNhs12851_bu_f0','CNhs12856_bu_f2','CNhs12857_bu_f2','CNhs12859_bu_f2','CNhs12920_bl_f2','CNhs12922_bu_f1','CNhs12952_bu_f0','CNhs13059_bl_f0','CNhs13060_bl_f1','CNhs13063_bl_f2','CNhs13063_bu_f1','CNhs13068_bl_f2','CNhs13099_bl_f0','CNhs13099_bu_f2','CNhs13156_bu_f0','CNhs13435_bu_f1','CNhs13439_bl_f1','CNhs13449_bl_f1','CNhs13458_bl_f1','CNhs13458_bl_f2','CNhs13458_bu_f2','CNhs13460_bu_f2','CNhs13464_bu_f2','CNhs13480_bl_f0','CNhs13498_bu_f1','CNhs13505_bu_f1','CNhs13549_bu_f2','CNhs13550_bl_f1','CNhs13793_bl_f2','CNhs13800_bu_f2','CNhs13801_bl_f2','CNhs13847_bu_f0','COE1_f2','CRACCWA,motif272','CRATCGC,motif590','CREB1_f1','CRX_Retina-Crx-ChIP-Seq/Homer','CSAAYWAG,motif787','CTACCAGTAC,motif314','CTACTTC,motif605','CTBGTCBTC,motif677','CTCCTGTTCC,motif443','CTCF_f2','CTCTCGATC,motif564','CTCTTAGTCATG,motif820','CTCTTCCAGTTC,motif857','CTSTTTCTTTAAG,motif929','CTTCTTTCC,motif732','DBP','DDIT3_f1','DMC1_Testis-DMC1-ChIP-Seq/Homer','E2F4_do','EBNA1_Raji-EBNA1-ChIP-Seq(GSE30709)/Homer','EGR1_K562-EGR1-ChIP-Seq/Homer','EOMES_f1','EPAS1_si','ESR1_do','ETV1_GIST48-ETV1-ChIP-Seq/Homer','EVI1_f1','FOSL2_f1','FOXA1_LNCAP-FOXA1-ChIP-Seq/Homer','FOXC2_f1','FOXD1_si','FOXM1','FOXO1_si','FOXP3','FOXP3_f1','FOX(C1,C2)','FUBP1_f1','GAAAAGC,motif664','GAAGSCG,motif658','GAATTSGA,motif806','GAGAGACAAAGG,motif729','GATA1..3','GATA1_si','GATCGCT,motif797','GATTGGTGCAG,motif851','GATTTTTWT,motif458','GAYCAGG,motif573','GCAGGAAACCACAG,motif220','GCCGCAAAC,motif342','GCCGCTTTAA,motif411','GCGCGCG,motif507','GCGGACTGAA,motif633','GCM1_f1','GCTCCGCTC,motif508','GFI1_f1','GGAAGAACTAG,motif201','GGACAAG,motif387','GGACCCCCTA,motif709','GGACCGCCG,motif717','GGAGKYTTAA,motif746','GGATGACGAA,motif197','GGCAACTTCT,motif638','GGGAATTTTTG,motif407','GGGGGAAAGAAA,motif661','GGGTGACTCGTA,motif209','GGGTTGCGTCA,motif101','GGTGACACAKC,motif113','GLI3_si','GTACGRC,motif321','GTAGATGTTGA,motif291','GTAGTCGA,motif591','GTATTAGG,motif834','GTCACCCTCA,motif402','GTGAATG,motif414','GTGACTSGG,motif114','GTTCCTATT,motif134','GTTGCTCAACAG,motif852','GTTGTAGCCC,motif679','GTWCAACA,motif210','GZF1','HES1_f1','HEY2_f1','HLTF_f1','HMGA2_f1','HNF1A','HNF4A_f1','HNF4G_f1','HNF6_f1','HOXC9_Ainv15-Hoxc9-ChIP-Seq/Homer','HOX(A5,B5)','HSF1_f2','HXA13_f1','HXB7_si','HXC8_f1','HXD13_f1','HXD4_f1','HXD9_f1','INSM1_f1','IRF2_f1','IRF5_f1','ISL1_f1','KAISO_f1','KCCGCCDY,motif582','KLF12','KLF4_mES-Klf4-ChIP-Seq/Homer','KLF8_f1','LHX2_f1','LHX3,4','MAFA_f1','MCR_f1','MEF2(A,B,C,D)','MEIS1_f2','MLXPL_f1','MSX2_f1','MTE(core)','MTF1_f1','MYBB_f1','MYB_ERMYB-Myb-ChIPSeq(GSE22095)/Homer','NAAAGTT,motif944','NANOG_mES-Nanog-ChIP-Seq/Homer','NEUROD1_Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer','NFAC2_f1','NFAT5_f1','NFATC1_motifA:Jurkat-NFATC1-ChIP-Seq/Homer','NFIX','NFKB1_REL_RELA','NFYB_f1','NKX2-1,4','NKX21_f1','NKX22_si','NKX3-2','NR0B1_si','NR1H4_f1','NR1I3_f2','NR1I3_si','NR2C2_Hela-TR4-ChIP-Seq/Homer','NR6A1_do','NRF1_MCF7-NRF1-ChIP-Seq/Homer','P73_si','PAX3_Rh4-PAX3:FKHR-ChIP-Seq/Homer','PAX4','PAX5_f1','PAX5_motifB:GM12878-PAX5-ChIP-Seq/Homer','PAX6_f1','PAX8_f1','PBX3_GM12878-PBX3-ChIP-Seq/Homer','PKNX1_si','PLAG1_f1','PLAG1_si','PO3F2_si','PO5F1_do','PO6F1_f1','POU1F1','POU3F1..4','POU5F1_mES-Oct4-ChIP-Seq/Homer','PRGR_f1','PROP1_f1','PRRX2_f1','PTF1A_f1','PURA_f1','RAGAGAGAGAGAG,motif269','RARA_f1','RARG_do','REST_f1','RFX1_NPC-Rfx1-ChIP-Seq/Homer','RGAAAGSAGAAG,motif654','RGCGGCSGC,motif262','RORA_f1','RRCGAACC,motif176','RREB1_si','RTATACTKT,motif723','RUNX1..3','RXR(A,B,G)','SGAGMKTAK,motif947','SMAD3_f1','SNAI2_f1','SOX17_f2','SOX18_f1','SOX2','SP1_f1','SP4_f1','SPDEF_VCaP-SPDEF-ChIP-Seq/Homer','SPZ1','SREBP1A_HepG2-Srebp1a-ChIP-Seq/Homer','SRF_do','STAT4_CD4-Stat4-ChIP-Seq/Homer','STCGWAG,motif238','STTCGVC,motif597','SUH_f1','TAACTGTACA,motif845','TACAGTATTC,motif699','TACCGGATC,motif263','TACCGGT,motif604','TACCTCCGC,motif788','TACTGYAG,motif560','TAGAMCCTAT,motif779','TAGGAAAC,motif60','TAGGCGA,motif945','TAGTCTGACG,motif940','TATCCCATT,motif724','TBP','TBX20_Heart-Tbx20-ChIP-Seq(GSE29636)/Homer','TBX3_f1','TBX5_HL1-Tbx5.biotin-ChIP-Seq/Homer','TCATCAGTTCC,motif933','TCATCCACATC,motif938','TCCTATTG,motif697','TCGCGCYG,motif706','TCKCGCT,motif355','TCSAGMT,motif441','TCSCGAGCTG,motif769','TCTCGCT,motif467','TCTCKCTC,motif323','TCTTCAA,motif816','TCTTCTTCTTC,motif479','TEAD1_f1','TEF','TF7L2_f1','TFCP2L1_mES-Tfcp2l1-ChIP-Seq/Homer','TFDP1','TGAATTGGCTG,motif563','TGACATCATAATG,motif44','TGACCAA,motif340','TGACGAA,motif9','TGCAGCATTA,motif668','TGGACGAA,motif481','TGGGAADTGTAGT,motif425','TGGTYCTMRT,motif814','TGIF1_f1','TGIF1_si','TGTGTGCG,motif245','THB_do','TKAAAGBGRCA,motif293','TLX1..3_NFIC(dimer)','TLX1_f1','TMCGYCR,motif946','TOPORS','TP53_Saos-p53-ChIP-Seq/Homer','TTAAGCGGC,motif366','TTATTCTGCTG,motif789','TTCCKGTCYG,motif829','TTCGTTCC,motif579','TTCTGCACC,motif618','TTCTTCAGCG,motif357','TTGATGATGATG,motif935','TTGCAGCGTA,motif613','TTGGCTCGGC,motif500','TTGGGRAATTTA,motif177','TTGTAGGT,motif707','TTHCTVTW,motif188','TTTTTCGCGGCT,motif429','TTYCGSTTC,motif442','TYTYTYTYTYYYYY,motif247','USF1_GM12878-Usf1-ChIP-Seq/Homer','VDR_f2','WYCKMKCG,motif815','YCYCTTT,motif332','YTCKCTT,motif512','YTGGTCCTGVT,motif924','ZBT7A_f1','ZBTB16','ZBTB4!METH_f1','ZBTB4_si','ZBTB6_si','ZEP2_si','ZFP161','ZN219_f1','ZN333_f1','ZN350_f1','ZN384_f1','ZN423_f1','ZN589_f1','ZNF143','motif10','motif1026','motif103','motif1032','motif1044','motif1049','motif106','motif1068','motif1097','motif11','motif119','motif123','motif125','motif134','motif136','motif143','motif145','motif162','motif177','motif183','motif189','motif196','motif198','motif199','motif210','motif218','motif222','motif233','motif238','motif247','motif252','motif260','motif261','motif263','motif27','motif282','motif29','motif290','motif293','motif297','motif3','motif30','motif300','motif301','motif307','motif313','motif316','motif324','motif33','motif335','motif351','motif357','motif359','motif361','motif365','motif37','motif373','motif378','motif382','motif41','motif415','motif424','motif432','motif44','motif440','motif441','motif443','motif445','motif459','motif46','motif461','motif463','motif468','motif475','motif477','motif478','motif486','motif489','motif494','motif498','motif499','motif515','motif516','motif517','motif527','motif550','motif553','motif554','motif558','motif560','motif561','motif563','motif568','motif57','motif577','motif585','motif588','motif602','motif606','motif61','motif614','motif624','motif627','motif64','motif647','motif66','motif660','motif667','motif668','motif670','motif679','motif680','motif682','motif684','motif686','motif688','motif74','motif75','motif77','motif80','motif816','motif822','motif827','motif830','motif835','motif837','motif839','motif843','motif858','motif861','motif867','motif87','motif882','motif885','motif886','motif890','motif895','motif897','motif898','motif9','motif90','motif906','motif909','motif915','motif929','motif931','motif935','motif943','motif944','motif950','motif953','motif956','motif957','motif963','motif965','motif969','motif97','motif970','motif977','motif981','motif990','motif991','motif999','motif_AAGTCN','motif_ACAGTN','motif_ACNGGT','motif_ACTGGN','motif_AGGGCN','motif_AGNCGT','motif_AGNCTT','motif_ANAGCT','motif_ANCAGT','motif_ANCGCT','motif_ANCTGT','motif_ANGACT','motif_ANGCCT','motif_ANGTCT','motif_ANTGCT','motif_ATGNCT','motif_ATNGCT','motif_CAAGTNNCA','motif_CACNGT','motif_CAGNAT','motif_CAGNCT','motif_CAGNGT','motif_CAGTNT','motif_CANCTG','motif_CANGTT','motif_CANTTG','motif_CATGNT','motif_CCAGCN','motif_CCANGT','motif_CCANTG','motif_CCCTNA','motif_CCNAGT','motif_CCNGAT','motif_CCNGCA','motif_CCNGGA','motif_CGACNT','motif_CGANCT','motif_CGNTGA','motif_CNAATG','motif_CNACTG','motif_CNAGGT','motif_CNAGTCTC','motif_CNAGTT','motif_CNATGG','motif_CNCAGT','motif_CNCATG','motif_CNGAAT','motif_CNGACT','motif_CNGATG','motif_CNGATT','motif_CNGCAG','motif_CNGCAT','motif_CNGCCA','motif_CNGGAT','motif_CNGGTA','motif_CTAGNG','motif_CTAGNT','motif_CTANGG','motif_CTATGN','motif_CTCANG','motif_CTGGGN','motif_CTGGNG','motif_CTNAGT','motif_CTNATG','motif_CTNGAT','motif_CTNTAG','motif_CTTANG','motif_CTTNAG','motif_GAACNT','motif_GAAGNT','motif_GACNCT','motif_GACNGT','motif_GACNTG','motif_GAGNCT','motif_GANACT','motif_GANCAT','motif_GANGTC','motif_GANTCT','motif_GANTTC','motif_GATCTN','motif_GATNTC','motif_GCAANT','motif_GCAATN','motif_GCACNT','motif_GCANTG','motif_GCNACT','motif_GCNCAT','motif_GCNGAT','motif_GCTCANGG','motif_GCTNAT','motif_GGACTN','motif_GGAGCN','motif_GGANTC','motif_GGCANT','motif_GGCNAT','motif_GGCNCA','motif_GGGACN','motif_GGNATC','motif_GGNCAT','motif_GNAATC','motif_GNACAT','motif_GNACCT','motif_GNACTT','motif_GNATCC','motif_GNATCT','motif_GNATTC','motif_GNCAAT','motif_GNCATC','motif_GNCATG','motif_GNCATT','motif_GNCTAG','motif_GNGAGC','motif_GNGCTA','motif_GNTACC','motif_GNTACT','motif_GNTCAT','motif_GTAANC','motif_GTACTN','motif_GTANCT','motif_GTCANC','motif_GTCANG','motif_GTCATN','motif_GTCNAG','motif_GTNACC','motif_GTNACT','motif_GTNATC','motif_GTNCAT','motif_GTNGAC','motif_GTTNAC','motif_TAACNG','motif_TAANGC','motif_TACANG','motif_TACTGN','motif_TAGCNG','motif_TAGGNC','motif_TAGNCT','motif_TAGNGC','motif_TAGNTC','motif_TAGTNC','motif_TANAGC','motif_TCAANG','motif_TCACNG','motif_TCAGNT','motif_TCCNGC','motif_TCNAGT','motif_TCNGAG','motif_TCNGGA','motif_TCTNAG','motif_TGAANC','motif_TGACNC','motif_TGACNG','motif_TGANAC','motif_TGANCT','motif_TGCNAG','motif_TGCTAN','motif_TGGAGN','motif_TGNACC','motif_TGNACT','motif_TGNCAC','motif_TGNCAT','motif_TGNCCA','motif_TGNCTA','motif_TGNGAC','motif_TGNTCA','motif_TGTANC','motif_TGTNAC','motif_TNAAGC','motif_TNAGCA','motif_TNAGCC','motif_TNAGGC','motif_TNATGC','motif_TNCAAG','motif_TNCACG','motif_TNCAGA','motif_TNCAGT','motif_TNCATG','motif_TNCGCA','motif_TNCTAG','motif_TNCTGA','motif_TNGACA','motif_TNGGAC','motif_TNGGCA','motif_TNTAGC','motif_TNTGCA','motif_TTACNG','motif_TTCANG','motif_TTCNGA','motif_TTGACN','motif_TTGCAN','motif_TTGNCA','motif_TTNAGC','motif_TTNCAG'];
var pval = [</html>{{{tfbs_overrepresentation}}}<html>];
var data = [];
var data = [];
for(i1=0;i1<motifs.length;i1++){
for(i1=0;i1<motifs.length;i1++){
Line 141: Line 126:
}
}


    $('#tfbs_overexpression_table').dataTable({
var tfbs_overexpression_table = $('#tfbs_overexpression_table').DataTable({
//"aaData": [["one", 1],["two", 3],["three", 0]],
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"sScrollY": "300px",
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
"bScrollCollapse": true,
scrollY: "300px",
"bPaginate": false,
        scrollCollapse: true,
"bFilter": false,
        pageLength: 10,
"bInfo": false,
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
"aaData": data,
data: data,
"aoColumns": [{ "sTitle": "Motifs", "sWidth": "200pt", "fnRender": function(obj) {
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 ) {
return sReturn = "<a href=\"/resource_browser/index.php/MacroAPE_1083:"+obj.aData[ obj.iDataColumn ]+"\">"+obj.aData[ obj.iDataColumn ]+"</a>";
                  var num =data;
} },{ "sTitle": "p-value" }],
                  var num_as_number=Number(num);
"aaSorting": [[ 1, "asc" ]],
                  return num_as_number.toFixed(2);
}}],
order: [[ 1, "desc" ]]
});
});
var tfbs_overexpression_jaspar_table= $('#tfbs_overexpression_jaspar').DataTable({
        dom: 'Blfrtip',
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scrollY: "300px",
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lengthMenu: [[10, 50, -1], [10, 50, "All"]],
columnDefs: [{ width: "200pt", render: function ( data, type, row, meta ) {return "<a href=\"/5/sstar/JASPAR_motif:"+data+"\">"+data+"</a>";}, targets: [ 0 ] }, {type: "numeric", targets: [ 1 ],render: function ( data, type, row, meta ) {
                  var num =data;
                  var num_as_number=Number(num);
                  return num_as_number.toFixed(2);
} }],
order: [[ 1, "desc" ]]
});
// tfbs results table end
// tf chipseq results table start
if($('#tf_chipseq_enrich')[0]){
    var tfbs_chipseq_enrich_table=$('#tf_chipseq_enrich').DataTable({
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order: [[4,'asc']],
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 ) {                   
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                  return exp_converter(num,2,"e");
} },{  type: "numeric", targets: [3],render: function ( data, type, row, meta ) {
                  var num =data;
                    return exp_converter(num,2,"e");
} },{type: "numeric", targets: [4],render: function ( data, type, row, meta ) {
                  var num =data;
                  return exp_converter(num,2,"e");
}}]
    });
}
// tf chipseq results table end
});
});
</script>
</script>
<table id="tfbs_overexpression_table"></table>
</html>
</html>




== ENCODE TF ChIP-seq peak enrichment analysis ==
Full id: [[full_id::{{{full_id}}}]]
{{#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}}  
{{#set:id={{{id}}}
}}
{{#set:cp_member_count={{#ask:[[Category:FFCP]][[Coexpression_cluster_id::{{{id}}}]]|format=count}}}}
{{#ifeq:{{#pos:{{PAGENAME}}|C}}|0
|{{#set:species=Human (Homo sapiens)}}
|{{#set:species=Mouse (Mus musculus)}}
}}
 
== Phase1 CAGE Peaks ==
{{#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}}
<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>[//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>
<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>
<html></thead><tbody></html>
{{#arraymap:{{{pathway_enrichment}}}|!|$
|<tr><td>{{#replace:$|;|</td><td>}}</td></tr>
|}}
<html></tbody></html></table>
|No results for this coexpression}}
<br><br>
{{Fontsize|3|Enriched Gene Ontology terms on this co-expression cluster}}{{#info:<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner
<br><br>link to source dataset
<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_GOstats.tar.gz  data]
}}
----
{{#switch:{{#show:{{FULLPAGENAME}}|?species}}
|Human (Homo sapiens)=
{{#ifeq:{{#sub:{{{gostat_on_coexpression_clusters}}}|0|2}}|GO|<span id="gostat_table_export_tool"></span>
<table id="gostat_table" class="stripe cell-border order-column compact"><html><thead></html><tr><th>GO ID</th><th>GO name</th><th>FDR corrected p-value</th></tr><html></thead><tbody></html>
<tr>
{{#arraymap:{{{gostat_on_coexpression_clusters}}}|$|$
|<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}}
|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>
{{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>
{{#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}}}|[//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}}}|[//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}}}|
<div style="float:left;width:33%;">
<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>
<html></thead><tbody></html>
{{#arraymap:{{{ontology_enrichment_celltype}}}|;|$
|{{#ifexist:{{#explode:$|!|0}}|<tr><td>[[{{#explode:$|!|0}}|{{#show:{{#explode:$|!|0}}|?name}}]]</td><td>{{#explode:$|!|1}}</td><td>{{#explode:$|!|2}}</td></tr>| }}
|}}
<html></tbody></html></table>
</div>
}}{{#if:{{{ontology_enrichment_uberon}}}|
<div style="float:left;width:33%;">
<table id="enrichment_list_uberon" class="stripe cell-border order-column compact"><caption class="table_title">Uber Anatomy</caption><html><thead></html>
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
<html></thead><tbody></html>{{#arraymap:{{{ontology_enrichment_uberon}}}|;|$
|{{#ifexist:{{#explode:$|!|0}}|<tr><td>[[{{#explode:$|!|0}}|{{#show:{{#explode:$|!|0}}|?name}}]]</td><td>{{#explode:$|!|1}}</td><td>{{#explode:$|!|2}}</td></tr>| }}
|}}
<html></tbody></html></table>
</div>
}}{{#if:{{{ontology_enrichment_disease}}}|
<div style="float:left;width:33%;">
<table id="enrichment_list_doid" class="stripe cell-border order-column compact"><caption class="table_title">Disease</caption><html><thead></html>
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
<html></thead><tbody></html>{{#arraymap:{{{ontology_enrichment_disease}}}|;|$
|{{#ifexist:{{#explode:$|!|0}}|<tr><td>[[{{#explode:$|!|0}}|{{#show:{{#explode:$|!|0}}|?name}}]]</td><td>{{#explode:$|!|1}}</td><td>{{#explode:$|!|2}}</td></tr>| }}
|}}
<html></tbody></html></table>
</div>
}}
<div style="clear:both;"></div>
 
 
{{#ifeq:{{#show:{{FULLPAGENAME}}|?species}}
|Human (Homo sapiens)
|{{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>
[//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>
[//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}}}
|<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
}} <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" 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><td>
{{#replace:{{#replace:{{{tfbs_overrepresentation_jaspar}}}|,|</td></tr><tr><td>}}|;|</td><td>}}
</td></tr>
<html></tbody></html>
</table>
|No results for this section
}}
|
}} <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>[//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">
}}
$(document).ready(function() {
----
    $('#tf_chipseq_enrich').dataTable({
{{#if: {{#pos:{{{tf_chipseq_enrich}}}|;}}  
"sScrollY": "300px",
|(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)<span id="tf_chipseq_enrich_table_export_tool"></span>  
"bPaginate": false,
<table id="tf_chipseq_enrich" class="stripe cell-border order-column compact"><html><thead></html><tr><th>TF</th><th>#promoters</th><th>Enrichment</th><th>p-value</th><th>q-value</th></tr><html></thead><tbody></html>
"bScrollCollapse": true,
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"aaSorting": [[4,'asc']],
"aoColumnDefs": [{"fnRender": function ( o, val ) {var elem = o.aData[0].split("#"); return "<a href=\"/resource_browser/EntrezGene:"+elem[1]+"\">"+elem[0]+"</a>";}, "aTargets": [ 0 ]}, { "sWidth": "150px", "sType": "numeric", "aTargets": [3] },{ "sWidth": "150px", "sType": "numeric", "aTargets": [4] }]
});
});
</script>
</html>
<table id="tf_chipseq_enrich"><html><thead></html><tr><th>TF</th><th>#promoters</th><th>Enrichment</th><th>p-value</th><th>q-value</th></tr><html></thead><tbody></html>
{{#arraymap:{{{tf_chipseq_enrich}}}|!|$
{{#arraymap:{{{tf_chipseq_enrich}}}|!|$
|{{#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 186: Line 324:
|No analysis results for this cluster
|No analysis results for this cluster
}}
}}
 
<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> 
== Coexpression_DPI_cluster_scores_median ==
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/coexpression_DPI_cluster_scores_median_human_Aug3_2012.txt.gz  data]}}
{{#info: <br>Analyst: }}
----
 
{{#ifexpr:{{#sub:{{{id}}}|1}} < 306|<html><script type="text/javascript">
{{#if: {{#pos:{{{coexpression_dpi_cluster_scores_median}}}|,}} |
<html>
<script type="text/javascript">
$(document).ready(function() {
$(document).ready(function() {
var data = [];
var data = [];
Line 202: Line 337:
data.push([ffsample[i1],values[i1]]);
data.push([ffsample[i1],values[i1]]);
}
}
 
  var coexpression_dpi_cluster_scores_median_table=  $('#coexpression_dpi_cluster_scores_median_table').DataTable({
    $('#coexpression_dpi_cluster_scores_median_table').dataTable({
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data: data,
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var elems = id.split('.');
"aaSorting": [[ 1, "desc" ]],
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}
},
{   title: "Score",
type: "numeric",
render: function ( data, type, row, meta ) {
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                  return num.toFixed(2);
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</script>
<table id="coexpression_dpi_cluster_scores_median_table"></table>
<table id="coexpression_dpi_cluster_scores_median_table" class="stripe cell-border order-column compact"></table>
</html>
</html>
|No analysis results for this cluster
{{#array_recordprops:coexpression_dpi_cluster_scores_median
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G4;11250,10409-106B4;10727,10638-108I8;11745,10636-108I6;11930,10513-107D9;11280,10420-106C6;10737,10082-102B1;11794,10014-101C5;10619,10070-101I7;11780,10452-106G2;11049,10453-106G3;11050,10449-106F8;11045,10042-101F6;10649,10069-101I6;11779,10193-103E4;12610,10631-108I1;11741,10438-106E6;11100,10488-107B2;11259,10196-103E7;12846,10071-101I8;11781,10071-101I8;12996,10041-101F5;10648,10451-106G1;11047,10450-106F9;11046,10604-108F1;11731,10605-108F2;11732,10606-108F3;11733,10603-108E9;11814,10497-107C2;11266,10448-106F7;11249,10643-109A4;11748,10426-106D3;10743,10431-106D8;10748,10197-103E8;12847,10443-106F2;11247,10815-111B5;12325,10816-111B6;12326,10817-111B7;12327,10015-101C6;10620,10410-106B5;10728,10054-101G9;11762,10758-110E2;11860,10711-109H9;11842,10040-101F4;10647,10470-106I2;11256,10415-106C1;10733,10198-103E9;12848,10614-108G2;11737,10612-108F9;11819,10549-107H9;11286,10615-108G3;11738,10487-107B1;11274,10433-106E1;10751,10688-109F4;11824,10444-106F3;11248,10444-106F3;11185,10485-107A8;11272,10413-106B8;10731,10175-103C4;13801,10161-103A8;12319,12131-128D7;12519,10624-108H3;11740,10712-109I1;11843,10205-103F7;12855,10206-103F8;12856,10207-103F9;12857,10050-101G5;11757,10051-101G6;11758,10016-101C7;10621,10046-101G1;10653,10778-110G4;11868,10633-108I3;11742,10818-111B8;12328,10819-111B9;12329,10820-111C1;12330,10484-107A7;11271,10808-111A7;11891,10169-103B7;13795,10153-102I9;12312,13425-144D5;13822,13433-144E4;13826,13437-144E8;13839,11904-125F5;13537,11905-125F6;13480,10039-101F3;10646,10791-110H8;11880,10017-101C8;10622,10045-101F9;10652,10509-107D5;11277,10839-111E2;12806,10692-109F8;11825,10079-102A7;11790,10078-102A6;11789,10721-110A1;11848,10569-108B2;11722,10570-108B3;11723,10571-108B4;11724,10647-109A8;11750,10752-110D5;11859,10782-110G8;11870,10726-110A6;11851,10018-101C9;10624,10086-102B5;11798,10182-103D2;13808,10165-103B3;12322,10499-107C4;11275,10408-106B3;10726,10019-101D1;10625,10068-101I5;11680,10075-102A3;11786,10077-102A5;11788,10727-110A7;11852,10775-110G1;11935,10412-106B7;10730,12231-129F8;12558,12232-129F9;12559,12233-129G1;12560,12234-129G2;12562,10414-106B9;10732,10170-103B8;13796,10183-103D3;13809,10150-102I6;12310,10174-103C3;13800,10155-103A2;12315,10038-101F2;10645,10838-111E1;12805,10759-110E3;11861,10514-107E1;11281,10465-106H6;11254,10691-109F7;11945,10843-111E6;12838,10844-111E7;12839,11747-123G1;12363,11748-123G2;12364,11749-123G3;12365,11750-123G4;12366,11751-123G5;12367,11840-124H4;13098,11752-123G6;12368,11753-123G7;12369,11754-123G8;12370,11755-123G9;12371,11756-123H1;12372,11833-124G6;13092,11760-123H5;12376,11836-124G9;13094,11758-123H3;12374,11835-124G8;13093,11762-123H7;12378,11838-124H2;13097,11757-123H2;12373,11759-123H4;12375,11761-123H6;12377,11842-124H6;13507,11837-124H1;13096,10568-108B1;11718,13230-141I8;13420,13231-141I9;13421,10696-109G3;12191,10493-107B7;11263,10494-107B8;11264,10850-111F4;13066,10851-111F5;13067,10852-111F6;13068,10853-111F7;13069,10854-111F8;13070,10855-111F9;13072,10856-111G1;13073,10847-111F1;13063,10846-111E9;13062,10848-111F2;13064,10845-111E8;13061,10857-111G2;13074,10858-111G3;13075,10156-103A3;12316,11901-125F2;13535,11902-125F3;13536,11903-125F4;13547,10689-109F5;11944,10648-109A9;11752,10784-110H1;11873,10744-110C6;11858,10772-110F7;11934,10474-106I6;11258,10600-108E6;11729,10684-109E9;11821,12226-129F3;12589,12227-129F4;12574,10508-107D4;11276,10539-107G8;11284,10607-108F4;11818,10555-107I6;11811,10774-110F9;11866,10637-108I7;11744,10663-109C6;11753,10728-110A8;11853,10729-110A9;11854,10430-106D7;10747,10730-110B1;12193,10813-111B3;11894,10812-111B2;11950,10037-101F1;10644,10172-103C1;13798,10163-103B1;12320,10076-102A4;11787,10073-102A1;11784,10036-101E9;10643,10195-103E6;12611,10277-104E7;13449,10434-106E2;10752,10550-107I1;11287,10545-107H5;11717,10544-107H4;11810,10704-109H2;11835,10510-107D6;11279,10558-107I9;11290,10020-101D2;10626,10732-110B3;11856,10049-101G4;11756,10698-109G5;11832,10437-106E5;11716,10417-106C3;10734,10035-101E8;10642,10171-103B9;13797,10157-103A4;12317,10034-101E7;10641,10072-101I9;11782,10199-103F1;12849,10200-103F2;12850,10697-109G4;11830,10723-110A3;11849,10179-103C8;13804,10160-103A7;12228,10180-103C9;13805,10162-103A9;12229,10021-101D3;10627,10840-111E3;12807,10706-109H4;11933,10033-101E6;10640,10032-101E5;10638,10490-107B4;11260,10439-106E7;11243,10022-101D4;10628,10176-103C5;12324,10469-106I1;11255,10067-101I4;11777,10411-106B6;10729,10471-106I3;11257,10030-101E3;10636,10475-106I7;11267,10787-110H4;11877,10477-106I9;11269,10695-109G2;11829,11771-123I7;12810,11772-123I8;12811,11773-123I9;12812,10093-102C3;11677,10442-106F1;11245,10442-106F1;11183,10201-103F3;12851,10639-108I9;11746,11843-124H7;13508,11841-124H5;13099,10693-109F9;11827,10436-106E4;10753,10483-107A6;11270,10282-104F3;13454,10023-101D5;10629,10066-101I3;11776,10065-101I2;11774,10800-110I8;11885,10610-108F7;11736,10841-111E4;12808,10541-107H1;11285,10842-111E5;12809,10562-108A4;11812,10024-101D6;10630,10064-101I1;11773,10609-108F6;11734,10048-101G3;11755,10781-110G7;11869,10181-103D1;13807,10159-103A6;12227,10056-101H2;11764,10737-110B8;11857,10025-101D7;10631,10044-101F8;10651,10424-106D1;10741,10463-106H4;11252,10616-108G4;11739,10486-107A9;11273,10062-101H8;11771,10202-103F4;12852,10158-103A5;12318,10441-106E9;11244,10031-101E4;10637,10063-101H9;11772,10063-101H9;12997,11763-123H8;12639,11765-123I1;12640,11768-123I4;12641,10807-111A6;11890,10790-110H7;11878,10798-110I6;11884,10786-110H3;11876,10591-108D6;12351,10593-108D8;12362,10590-108D5;11726,10026-101D8;10632,10096-102C6;12998,10168-103B6;13794,10154-103A1;12314,10209-103G2;12858,10061-101H7;11770,10027-101D9;10633,10043-101F7;10650,10783-110G9;11872,10028-101E1;10634,10060-101H6;11769,10203-103F5;12853,10059-101H5;11768,10047-101G2;10654,10029-101E2;10635,10058-101H4;11766,10418-106C4;10735,10492-107B6;11261,10694-109G1;11828,10797-110I5;11883,10057-101H3;11765,10100-102D1;11676,10055-101H1;11763,10204-103F6;12854,10191-103E2;12844,10563-108A5;11813
|{{{coexpression_dpi_cluster_scores_median}}}
}}
|This analysis result is provided for C0 - C305 clusters.
}}
}}




[[Category:Coexpression_clusters]]
[[Category:Coexpression_clusters]]

Latest revision as of 11:59, 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 "{".

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