Template:Coexpression clusters: Difference between revisions
From FANTOM5_SSTAR
mNo edit summary |
No edit summary |
||
| (2 intermediate revisions by the same user not shown) | |||
| Line 21: | Line 21: | ||
dom: 'Blfrtip', | dom: 'Blfrtip', | ||
lengthMenu: [[10, 25, 50, -1], [10, 25, 50, "All"]], | lengthMenu: [[10, 25, 50, -1], [10, 25, 50, "All"]], | ||
buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'] | buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | ||
columns: [{title:"Id"},{title:"Short description"}] | |||
}); | }); | ||
// FFCP list end | // FFCP list end | ||
| Line 36: | Line 37: | ||
columnDefs: [{render: function ( data, type, row, meta ) { | columnDefs: [{render: function ( data, type, row, meta ) { | ||
var name = data.split(":"); | var name = data.split(":"); | ||
if(name[0].indexOf("KEGG") != -1){ | 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{ | ||
| Line 51: | Line 52: | ||
}, targets: [ 4 ]}, { type: "numeric", targets: [0,1], render: function ( data, type, row, meta ) { | }, targets: [ 4 ]}, { type: "numeric", targets: [0,1], render: function ( data, type, row, meta ) { | ||
var num =data; | var num =data; | ||
return exp_converter(num,2,"e") ; | return exp_converter(num,2,"e"); | ||
} }] | } }] | ||
}); | }); | ||
| Line 73: | Line 74: | ||
render: function ( data, type, row, meta ) { | render: function ( data, type, row, meta ) { | ||
var num =data; | var num =data; | ||
return exp_converter(num,2,"e") ; | return exp_converter(num,2,"e"); | ||
} }] | } }] | ||
}); | }); | ||
| Line 136: | Line 137: | ||
var num =data; | 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); | ||
}}], | }}], | ||
order: [[ 1, "desc" ]] | order: [[ 1, "desc" ]] | ||
| Line 151: | Line 152: | ||
var num =data; | 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); | ||
} }], | } }], | ||
order: [[ 1, "desc" ]] | order: [[ 1, "desc" ]] | ||
| Line 169: | Line 170: | ||
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 ) { | 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 ) { | ||
var num =data; | var num =data; | ||
return exp_converter(num,2,"e") ; | return exp_converter(num,2,"e"); | ||
} },{ type: "numeric", targets: [3],render: function ( data, type, row, meta ) { | } },{ type: "numeric", targets: [3],render: function ( data, type, row, meta ) { | ||
var num =data; | var num =data; | ||
return exp_converter(num,2,"e") ; | return exp_converter(num,2,"e"); | ||
} },{type: "numeric", targets: [4],render: function ( data, type, row, meta ) { | } },{type: "numeric", targets: [4],render: function ( data, type, row, meta ) { | ||
var num =data; | var num =data; | ||
return exp_converter(num,2,"e") ; | return exp_converter(num,2,"e"); | ||
}}] | }}] | ||
}); | }); | ||
| Line 195: | Line 196: | ||
== Phase1 CAGE Peaks == | == Phase1 CAGE Peaks == | ||
{{#ask:[[Category:FFCP]][[FFCP_PHASE2:+]][[Species::Human (Homo sapiens)]][[Coexpression_cluster_id::{{{id}}}]]|?Short_description|format= | {{#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> | <br> | ||
| Line 202: | Line 203: | ||
<br> | <br> | ||
<br>link to source dataset | <br>link to source dataset | ||
<br>[ | <br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_modules.tar.gz data] | ||
}} | }} | ||
---- | ---- | ||
| Line 217: | Line 218: | ||
{{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 | {{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><br>link to source dataset | ||
<br>[ | <br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_GOstats.tar.gz data] | ||
}} | }} | ||
---- | ---- | ||
| Line 246: | Line 247: | ||
{{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}}}|[ | {{#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}}}|[ | {{#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}}}|[ | {{#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> | ||
}} | }} | ||
---- | ---- | ||
| Line 287: | Line 288: | ||
|{{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> | |{{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> | 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> | <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] | ||
}} | }} | ||
---- | ---- | ||
| Line 311: | Line 312: | ||
{{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 | {{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 | ||
<br><br>link to source dataset<br> | <br><br>link to source dataset<br> | ||
<br>[ | <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] | ||
}} | }} | ||
---- | ---- | ||
| Line 326: | Line 327: | ||
<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> | {{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> | ||
[ | [//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/coexpression_DPI_cluster_scores_median_human_Aug3_2012.txt.gz data]}} | ||
---- | ---- | ||
{{#ifexpr:{{#sub:{{{id}}}|1}} < 306|<html><script type="text/javascript"> | {{#ifexpr:{{#sub:{{{id}}}|1}} < 306|<html><script type="text/javascript"> | ||
| Line 356: | Line 357: | ||
render: function ( data, type, row, meta ) { | render: function ( data, type, row, meta ) { | ||
var num =data; | var num =data; | ||
return num.toFixed(2) ; | return num.toFixed(2); | ||
} | } | ||
}], | }], | ||
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>
| Ontology term | p-value | n |
|---|
| Ontology term | p-value | n |
|---|
| Ontology term | p-value | n |
|---|
ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data
No analysis results for this cluster
Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data
Expression error: Unrecognized punctuation character "{".
