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// GOstat results table start
// sample list for relative expression
    var oTable = $('#gostat_table').dataTable({
var rexp_sample = ["Atoh1%2b%20Inner%20ear%20hair%20cells%20-%20organ%20of%20corti%2c%20pool1.CNhs12533.12158-128G7","CD326%2b%20enterocyte%20isolated%20from%20mice%2c%20treated%20with%20RANKL%2c%20day03%2c%20pool1.CNhs13242.11850-124I5","CD326%2b%20enterocyte%20isolated%20from%20mice%2c%20treated%20with%20RANKL%2c%20day03%2c%20pool2.CNhs13233.11851-124I6","CD326%2b%20enterocyte%2c%20pool1.CNhs13542.11848-124I3","CD326%2b%20enterocyte%2c%20pool2.CNhs13197.11849-124I4","CD326%2b%2b%20enterocyte%20isolated%20from%20mice%2c%20treated%20with%20RANKL%2c%20day03%2c%20pool1.CNhs13236.11852-124I7","CD326%2b%2b%20enterocyte%20isolated%20from%20mice%2c%20treated%20with%20RANKL%2c%20day03%2c%20pool2.CNhs13210.11853-124I8","CD4%2bCD25%2b%20regulatory%20T%20cells%2c%20pool2%20%28Balb_cAJcl%29.CNhs13221.11818-124E9","CD4%2bCD25-CD44-%20naive%20conventional%20T%20cells%2c%20PMA%20and%20ionomycin%20stimulation%2c%2002hr%2c%20pool1%20%28C57BL_6J%29.CNhs13219.11816-124E7","CD4%2bCD25-CD44-%20naive%20conventional%20T%20cells%2c%20PMA%20and%20ionomycin%20stimulation%2c%2002hr%2c%20pool2%20%28Balb_cAJcl%29.CNhs13226.11820-124F2","CD4%2bCD25-CD44-%20naive%20conventional%20T%20cells%2c%20antiCD3_CD28%20stimulation%2c%2006hr%2c%20pool1%20%28C57BL_6J%29.CNhs13218.11815-124E6","CD4%2bCD25-CD44-%20naive%20conventional%20T%20cells%2c%20antiCD3_CD28%20stimulation%2c%2006hr%2c%20pool2%20%28Balb_cAJcl%29.CNhs13225.11819-124F1","CD4%2bCD25-CD44-%20naive%20conventional%20T%20cells%2c%20pool1%20%28C57BL_6J%29.CNhs13217.11813-124E4","CD4%2bCD25-CD44-%20naive%20conventional%20T%20cells%2c%20pool2%20%28Balb_cAJcl%29.CNhs13220.11817-124E8","CD41%2b%20megakaryocyte%20cancer%2c%20donor1.CNhs13079.11774-124A1","CD41%2b%20megakaryocyte%20cancer%2c%20donor2.CNhs13213.11776-124A3","CD41%2b%20megakaryocyte%20cancer%2c%20donor3.CNhs13506.11778-124A5","CD41%2b%20megakaryocyte%20control%2c%20donor1.CNhs13212.11775-124A2","CD41%2b%20megakaryocyte%20control%2c%20donor2.CNhs13214.11777-124A4","CD41%2b%20megakaryocyte%20control%2c%20donor3.CNhs13201.11779-124A6","Clontech%20Mouse%20Universal%20Reference%20Total%20RNA%2c%20pool1.CNhs10609.10001-101A3","EBF%20KO%20HPCs%20induced%20to%20T%20cell%2c%2000hr00min%2c%20biol_rep1.CNhs11058.12972-138H2","EBF%20KO%20HPCs%20induced%20to%20T%20cell%2c%2000hr00min%2c%20biol_rep2.CNhs12980.12988-138I9","Follicle%20Associated%20Epithelium%2c%20pool2.CNhs13211.10262-104D1","Follicle%20Associated%20Epithelium%2c%20pool3.CNhs13200.10263-104D2","GP2%2b%20M%20cell%2c%20pool1.CNhs13228.11845-124H9","GP2%2b%20M%20cell%2c%20pool2.CNhs13231.11846-124I1","GP2%2b%20M%20cell%2c%20pool3.CNhs13240.11847-124I2","Ileum%20epithelium%2c%20pool1.CNhs13199.10252-104B9","Ileum%20epithelium%2c%20pool2.CNhs13232.10253-104C1","Ileum%20epithelium%2c%20treated%20with%20RANKL%2c%20day03%2c%20pool3.CNhs13234.10260-104C8","J2E%20erythroblastic%20leukemia%20response%20to%20erythropoietin%2c%2000hr00min%2c%20biol_rep1.CNhs12449.13063-139I3","J2E%20erythroblastic%20leukemia%20response%20to%20erythropoietin%2c%2000hr00min%2c%20biol_rep2.CNhs12668.13129-140G6","J2E%20erythroblastic%20leukemia%20response%20to%20erythropoietin%2c%2000hr00min%2c%20biol_rep3.CNhs12770.13195-141E9","Lgr5%20positive%20intestinal%20stem%20cells%2c%20pool1.CNhs12555.12228-129F5","Lgr5%20positive%20intestinal%20stem%20cells%2c%20pool2.CNhs12556.12229-129F6","Lgr5%20positive%20intestinal%20stem%20cells%2c%20pool3.CNhs12557.12230-129F7","MC1%2bGr1%2b%20myeloid-derived%20suppressor%20cells%20cancer%2c%20donor1%20%2810%2c11%2c12%203LL%29.CNhs12539.12159-128G8","MC1%2bGr1%2b%20myeloid-derived%20suppressor%20cells%20cancer%2c%20donor2%20%280127%203LL%29.CNhs12198.12161-128H1","MC1%2bGr1%2b%20myeloid-derived%20suppressor%20cells%20cancer%2c%20donor3%20%280128%203LL%29.CNhs12542.12163-128H3","MC1%2bGr1%2b%20myeloid-derived%20suppressor%20cells%20control%2c%20donor1%20%284%2c5%2c6PBS%29.CNhs12540.12160-128G9","MC1%2bGr1%2b%20myeloid-derived%20suppressor%20cells%20control%2c%20donor2%20%280127%20PBS%29.CNhs12541.12162-128H2","MC1%2bGr1%2b%20myeloid-derived%20suppressor%20cells%20control%2c%20donor3%20%280128%20PBS%29.CNhs12543.12164-128H4","Mouse%20Aortic%20Smooth%20Muscle%20cells%20-%20differentiated%2c%20biol_rep1.CNhs11055.11484-119D8","Mouse%20Aortic%20Smooth%20Muscle%20cells%20-%20differentiated%2c%20biol_rep2.CNhs11056.11485-119D9","Mouse%20Aortic%20Smooth%20Muscle%20cells%2c%20donor1.CNhs11297.11299-117B3","Mouse%20Astrocytes%20-%20cerebellar%2c%20donor1.CNhs13077.11708-123B7","Mouse%20Astrocytes%20-%20cerebellar%2c%20donor2.CNhs12076.11550-120C2","Mouse%20Astrocytes%20-%20hippocampus%2c%20donor1.CNhs12129.11709-123B8","Mouse%20Astrocytes%20-%20hippocampus%2c%20donor2.CNhs12077.11551-120C3","Mouse%20Astrocytes%2c%20donor2.CNhs12078.11552-120C4","Mouse%20Astrocytes%2c%20donor3.CNhs12107.11633-122C4","Mouse%20CD19%2b%20B%20Cells%2c%20donor1.CNhs13531.11856-125A2","Mouse%20CD4%2b%20T%20Cells%2c%20donor1.CNhs13509.11854-124I9","Mouse%20CD8%2b%20T%20Cells%2c%20donor1.CNhs13511.11855-125A1","Mouse%20Cardiac%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y%2c%20embryo%20E17%2e5%2c%20pool1%20%28internal%20control%29.CNhs11246.3139-67G5","whole%20body%2c%20embryo%20E17%2e5%2c%20pool1%20%28internal%20control%29.CNhs11278.3139-67G5","whole%20body%2c%20embryo%20E17%2e5.CNhs10513.490-9F9","whole%20body%2c%20embryo%20E17.CNhs10517.475-3I5","whole%20body%2c%20embryo%20E18.CNhs10516.493-3B3","whole%20body%2c%20neonate%20N00.CNhs10525.657-19C2","whole%20body%2c%20neonate%20N01.CNhs10576.659-23C6","whole%20body%2c%20neonate%20N06.CNhs10515.692-21D1","whole%20body%2c%20neonate%20N10.CNhs10518.761-6B4"];
"iDisplayLength": 10,
 
"aLengthMenu": [[25, 50, -1], [25, 50, "All"]],
// median table
"aoColumnDefs": [ { "sType": "numeric", "aTargets": [2] }],
var rexp_median_data = [];
"aaSorting": [[2,'asc']]
var rexp_median_values = [</html>{{{coexpression_dpi_cluster_scores_median}}}<html>];
//var rexp_median_values = ["0.003","200","1.36e-30"];
for(i1=0;i1<389;i1++){
rexp_median_data.push([rexp_sample[i1], rexp_median_values[i1]]);
}
  var coexpression_dpi_cluster_scores_table =  $('#coexpression_dpi_cluster_scores_median_table').DataTable({
        dom: 'Blfrtip',
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
scrollY: "300px",
        scrollCollapse: true,
        pageLength: 10,
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
data: rexp_median_data,
columns: [{ title: "FF samples",  orderable: false, render: function ( data, type, row, meta ) {
var id = data;
var elems = id.split('.');
return "<a href=\"/5/sstar/FF:"+elems[2]+"\">"+decodeURIComponent(elems[0])+" "+elems[1]+"</a>";
} },{ title: "Score", type: "html-num" ,render: function ( data, type, row, meta ) {
              var num = data;
              var numb = new Number(num);
                  return numb.toFixed(2);
} }],
order: [[ 1, "desc" ]],
});
 
// ontology enrichment table
 
$('.enrichment_list').DataTable({
        dom: 'lfrtip',
scrollY: "300px",
        scrollCollapse: true,
        pageLength: 10,
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
columnDefs: [{ ordarable: false, targets: [ 0 ] },  { type: "html-num", targets: [1] }, { width: "50pt", targets: [ 1 ] }],
order: [[ 1, "asc" ]]
});
});


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"} ]});


$('#gostat_table_export_tool').before( oTableTools.dom.container );
// ffcp list
// GOstat results table end
var ffcp_list_table=$('.ffcp_list').DataTable({
        dom: 'Blfrtip',
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
lengthMenu: [[10, 25, 50, 100], [10, 25, 50, 100]],
order: [[ 0, "asc" ]]
});


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


== Phase1 CAGE Peaks ==
{{#ask:[[Category:FFCP]][[FFCP_PHASE2:+]][[Species::Mouse (Mus musculus)]][[MCL_coexpression_id::{{PAGENAME}}]]|?Short_description|format=ttable|class=ffcp_list stripe cell-border order-column compact|limit=20000}}
<br>


{{#set:MCL_coexpression_id={{{PAGENAME}}}}}
{{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/mm9_co-expression_modules.tar.gz  data]
}}
<br>
----
{{#if:{{{gostat_on_MCL_coexpression}}}|
<html>
<script type="text/javascript">
$(document).ready(function() {


// GOstat results table start
    var oTable =  $('#gostat_table').DataTable({
        dom: 'Blfrtip',
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
        scrollY: "300px",
        scrollCollapse: true,
        pageLength: 10,
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
columnDefs: [ { type: "html-num", targets: [2],render: function ( data, type, row, meta ) {
                  var num =data;
                  return exp_converter(num,2,"e");
} }],
order: [[2,'asc']]
});


== Phase1 CAGE Peaks ==
// GOstat results table end
});
</script>
</html>


 
<table id="gostat_table" class="stripe cell-border order-column compact"><html><thead></html><tr><th>GO ID</th><th>GO name</th><th>FDR corrected p-value</th></tr><html></thead><tbody></html>
== GOStat results on Coexpression cluster  ==
{{#info:The results for GOStat analysis on co-expressed clusters("All" category).  <br>Analyst: Erik Arner}}
{{#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>
<tr>
<tr>
{{#arraymap:{{{gostat_on_MCL_coexpression}}}|!|$
{{#arraymap:{{{gostat_on_MCL_coexpression}}}|!|$
Line 49: Line 120:
|no results for this coexpression
|no results for this coexpression
}}
}}
<br><br>
{{Fontsize|3|Relative expression of the co-expression cluster over median }}{{#info: <br>Analyst: }}
----
<div id="relative_exp_of_coexp_table_button"></div><br>
<table id="coexpression_dpi_cluster_scores_median_table" class="stripe cell-border order-column compact"></table>
{{#array_recordprops:coexpression_dpi_cluster_scores_median
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|{{{coexpression_dpi_cluster_scores_median}}}
}}
<br><br>
{{Fontsize|3|Enriched sample ontology terms on this co-expression cluster}}{{#info:<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji
<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_mm9_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_mm9_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_mm9_clusters_relative_exp_enrichment_disease.txt.gz  disease_data]|}}<br>
}}
----
{{#if:{{{ontology_enrichment_celltype}}}|
<div style="float:left;width:33%;">
<table class="enrichment_list stripe cell-border order-column compact" id="enrichment_list_cell_type_table"><caption class="table_title">Cell Type</caption><html><thead></html>
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
<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:$|!|2}}</td></tr>| }}
|
}}
<html></tbody></html></table>
</div>
}}{{#if:{{{ontology_enrichment_uberon}}}|
<div style="float:left;width:33%;">
<table class="enrichment_list stripe cell-border order-column compact" id="enrichment_list_uberon_table"><caption class="table_title">Uber Anatomy</caption><html><thead></html>
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
<html></thead><tbody></html>
{{#arraymap:{{{ontology_enrichment_uberon}}}|;|$
|{{#ifexist:{{#explode:$|!|0}}|<tr><td>[[{{#explode:$|!|0}}|{{#show:{{#explode:$|!|0}}|?name}}]]</td><td>{{#explode:$|!|1}}</td><td>{{#explode:$|!|2}}</td></tr>| }}
|}}
<html></tbody></html></table>
</div>
}}{{#if:{{{ontology_enrichment_disease}}}|
<div style="float:left;width:33%;">
<table class="enrichment_list stripe cell-border order-column compact" id="enrichment_list_disease_table"><caption class="table_title">Disease</caption><html><thead></html>
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
<html></thead><tbody></html>
{{#arraymap:{{{ontology_enrichment_disease}}}|;|$
|{{#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>
<br>
{{Fontsize|3|TFBS overrepresentation}}{{#info:<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>
link to source data <br> Novel motifs <br>
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9.novel_motif.coexpression_clusters_overrepresentation.txt.gz data] <br>
<br> Jaspar motifs <br>
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz data]
}}
----
<html>
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{{#set:cp_member_count={{#ask:[[Category:FFCP]][[Species::Mouse (Mus musculus)]][[MCL_coexpression_id::{{PAGENAME}}]]|format=count}}}}
[[Category:MCL_coexpression_mm9]]
[[Category:MCL_coexpression_mm9]]

Latest revision as of 20:14, 4 July 2023


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

GO IDGO nameFDR corrected p-value
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Relative expression of the co-expression cluster over median <br>Analyst:


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

Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs




JASPAR motifs


Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}

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