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Template:MCL coexpression mm9: Difference between revisions

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{{Loading|loadingimage=sprites.gif}}<html>
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rexp_median_data.push([rexp_sample[i1], rexp_median_values[i1]]);
rexp_median_data.push([rexp_sample[i1], rexp_median_values[i1]]);
}
}
   var coexpression_dpi_cluster_scores_table =  $('#coexpression_dpi_cluster_scores_median_table').dataTable({
   var coexpression_dpi_cluster_scores_table =  $('#coexpression_dpi_cluster_scores_median_table').DataTable({
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               var num = data;
               var num =obj.aData[obj.iDataColumn];
               var numb = new Number(num);
               var numb = new Number(num);
                   return numb.toFixed(2) ;
                   return numb.toFixed(2);
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$('#relative_exp_of_coexp_table_button').before(coexpression_dpi_cluster_scores_table_tool.dom.container );


// ontology enrichment table
// ontology enrichment table


$('.enrichment_list').dataTable({
$('.enrichment_list').DataTable({
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});
});




// ffcp list
// ffcp list
var ffcp_list_table=$('.ffcp_list').dataTable();
var ffcp_list_table=$('.ffcp_list').DataTable({
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});


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


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<br>
<br>
<br>link to source dataset
<br>link to source dataset
<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_modules.tar.gz  data]
<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_modules.tar.gz  data]
}}
}}
----
<br>
<br>
{{Fontsize|3|Enriched Gene Ontology terms on this co-expression cluster}}{{#info:<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner
<br><br>link to source dataset
<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_GOstats.tar.gz  data]
}}
----
----
{{#if:{{{gostat_on_MCL_coexpression}}}|
{{#if:{{{gostat_on_MCL_coexpression}}}|
Line 100: Line 91:


// GOstat results table start
// GOstat results table start
     var oTable =  $('#gostat_table').dataTable({
     var oTable =  $('#gostat_table').DataTable({
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                   var num =data;
                   var num =obj.aData[obj.iDataColumn];
                   return exp_converter(num,2,"e");
                   return exp_converter(num,2,"e");
} }],
} }],
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order: [[2,'asc']]
});
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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 );
// GOstat results table end
// GOstat results table end
});
});
Line 123: Line 110:
</html>
</html>


<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>
<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}}}|!|$
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----
----
<div id="relative_exp_of_coexp_table_button"></div><br>
<div id="relative_exp_of_coexp_table_button"></div><br>
<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>
{{#array_recordprops:coexpression_dpi_cluster_scores_median
{{#array_recordprops:coexpression_dpi_cluster_scores_median
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{{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  
{{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>
<br><br>links to source dataset<br><br>
{{#if:{{{ontology_enrichment_celltype}}}|[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/mcl_mm9_clusters_relative_exp_enrichment_cell_type.txt.gz  cell_data]|}}<br>
{{#if:{{{ontology_enrichment_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}}}|[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/mcl_mm9_clusters_relative_exp_enrichment_uberon.txt.gz  uberon_data]|}}<br>
{{#if:{{{ontology_enrichment_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}}}|[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/mcl_mm9_clusters_relative_exp_enrichment_disease.txt.gz  disease_data]|}}<br>
{{#if:{{{ontology_enrichment_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}}}|
{{#if:{{{ontology_enrichment_celltype}}}|
<div style="float:left;width:33%;">
<div style="float:left;width:33%;">
<table class="enrichment_list" id="enrichment_list_cell_type_table"><caption class="table_title">Cell Type</caption><html><thead></html>
<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>
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
<html></thead><tbody></html>
<html></thead><tbody></html>
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}}{{#if:{{{ontology_enrichment_uberon}}}|
}}{{#if:{{{ontology_enrichment_uberon}}}|
<div style="float:left;width:33%;">
<div style="float:left;width:33%;">
<table class="enrichment_list" id="enrichment_list_uberon_table"><caption class="table_title">Uber Anatomy</caption><html><thead></html>
<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>
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
<html></thead><tbody></html>
<html></thead><tbody></html>
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}}{{#if:{{{ontology_enrichment_disease}}}|
}}{{#if:{{{ontology_enrichment_disease}}}|
<div style="float:left;width:33%;">
<div style="float:left;width:33%;">
<table class="enrichment_list" id="enrichment_list_disease_table"><caption class="table_title">Disease</caption><html><thead></html>
<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>
<tr><th>Ontology term</th><th>p-value</th><th>n</th></tr>
<html></thead><tbody></html>
<html></thead><tbody></html>
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{{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>
{{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>
link to source data <br> Novel motifs <br>
[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9.novel_motif.coexpression_clusters_overrepresentation.txt.gz data] <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>
<br> Jaspar motifs <br>
[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz data]
[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz data]
}}
}}
----
----
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}
}


  var tfbs_overexpression_novel_table_obj=  $('#tfbs_overexpression_table').dataTable({
  var tfbs_overexpression_novel_table_obj=  $('#tfbs_overexpression_table').DataTable({
//"aaData": [["one", 1],["two", 3],["three", 0]],
        dom: 'Blfrtip',
"sScrollY": "300px",
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
                "bScrollCollapse": true,
scrollY: "300px",
"bPaginate": true,
        scrollCollapse: true,
"bFilter": true,
        pageLength: 10,
"bInfo": true,
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
                "iDisplayLength": 10,
        data: data,
"aLengthMenu": [[10, 50, -1], [10, 50, "All"]],
        columns: [{ title: "Motifs", width: "300pt", orderable: true, render: function ( data, type, row, meta ) {
                "aaData": data,
var id = data;
                "aoColumns": [{ "sTitle": "Motifs", "sWidth": "300pt", "bSortable": true, "fnRender": function(obj) {
        var elems = id.split('_')[0];  
var id = obj.aData[ obj.iDataColumn ];
        var motif_id=elems.substr(5,elems.length);
                var elems = id.split('_')[0];  
  return "<a href=\"/5/sstar/Novel_motif:"+motif_id+"\">"+decodeURIComponent(id)+"</a>";
                            var motif_id=elems.substr(5,elems.length);
  return sReturn = "<a href=\"/resource_browser/Novel_motif:"+motif_id+"\">"+decodeURIComponent(id)+"</a>";
              } },
              } },
                             { "sTitle": "-log10(p-value)","sType": "numeric","fnRender": function (obj) {                  
                             { title: "-log10(p-value)",type: "html-num",render: function ( data, type, row, meta ) {
                   var num =obj.aData[obj.iDataColumn];
                   var num =data;
                   var num_as_number=Number(num);
                   var num_as_number=Number(num);
                   return num_as_number.toFixed(2) ;
                   return num_as_number.toFixed(2);
} }],
} }],
                 "aaSorting": [[ 1, "desc" ]]
                 order: [[ 1, "desc" ]]
});
});
var tfbs_overexpression_novel_table_objtool = new TableTools(  tfbs_overexpression_novel_table_obj, {"sSwfPath": "/resource_browser/rb_js/datatables/extras/TableTools/media/swf/copy_csv_xls_pdf.swf", "aButtons": [ {"sExtends": "copy", "mColumns": "visible"},{"sExtends": "csv", "mColumns": "visible"}, {"sExtends": "pdf", "mColumns": "visible"} ]});
$('#tfbs_overexpression_novel_table_button').before( tfbs_overexpression_novel_table_objtool.dom.container );


  tfbs_overexpression_jaspar_table_obj=$('#tfbs_overexpression_jaspar').dataTable({
  tfbs_overexpression_jaspar_table_obj=$('#tfbs_overexpression_jaspar').DataTable({
"sScrollY": "300px",
        dom: 'Blfrtip',
                "bScrollCollapse": true,
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
"bPaginate": true,
scrollY: "300px",
"bFilter": true,
        scrollCollapse: true,
"bInfo": true,
        pageLength: 10,
                "iDisplayLength": 10,
lengthMenu: [[10, 50, -1], [10, 50, "All"]],
"aLengthMenu": [[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: "html-num", targets: [ 1 ],render: function ( data, type, row, meta ) {
"aoColumnDefs": [{ "sWidth": "200pt", "fnRender": function ( o, val ) {return "<a href=\"/resource_browser/JASPAR_motif:"+o.aData[0]+"\">"+o.aData[0]+"</a>";}, "aTargets": [ 0 ] }, {"sType": "numeric", "aTargets": [ 1 ],"fnRender": function (obj) {                  
                   var num =data;
                   var num =obj.aData[obj.iDataColumn];
                   var num_as_number=Number(num);
                   var num_as_number=Number(num);
                   return num_as_number.toFixed(2) ;
                   return num_as_number.toFixed(2) ;
} }],
} }],
"aaSorting": [[ 1, "desc" ]]
order: [[ 1, "desc" ]]
});
});
tfbs_overexpression_jaspar_table_objtool = new TableTools( tfbs_overexpression_jaspar_table_obj, {"sSwfPath": "/resource_browser/rb_js/datatables/extras/TableTools/media/swf/copy_csv_xls_pdf.swf", "aButtons": [ {"sExtends": "copy", "mColumns": "visible"},{"sExtends": "csv", "mColumns": "visible"}, {"sExtends": "pdf", "mColumns": "visible"} ]});
$('#tfbs_overexpression_jaspar_table_button').before(tfbs_overexpression_jaspar_table_objtool.dom.container );
});
});
</script>
</script>
Line 252: Line 229:
{{Fontsize|3|Novel motifs}}
{{Fontsize|3|Novel motifs}}
<div id="tfbs_overexpression_novel_table_button"></div><br>
<div id="tfbs_overexpression_novel_table_button"></div><br>
<table id="tfbs_overexpression_table"></table><br><br>
<table id="tfbs_overexpression_table" class="stripe cell-border order-column compact"></table><br><br>
{{Fontsize|3|JASPAR motifs}}
{{Fontsize|3|JASPAR motifs}}
<div id="tfbs_overexpression_jaspar_table_button"></div><br>
<div id="tfbs_overexpression_jaspar_table_button"></div><br>
<table id="tfbs_overexpression_jaspar"><html><thead></html>
<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><th>Motifs</th><th>-log10(p-value)</th></tr><html></thead><tbody></html>
<tr><td>
<tr><td>

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
{{{gostat_on_MCL_coexpression}}}



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


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

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

Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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

Novel motifs




JASPAR motifs


Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}

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