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Coexpression cluster:C1655: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;5:7.97114762582482:3.10621793420244e-05:0.00062833680966525!EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00110693270718678!FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000388738853617863!GATA2#2624;5:12.744931733554:2.9719152914525e-06:0.000101102234893814!JUN#3725;5:12.5128291923363:3.25800591331781e-06:0.00010902367176578!JUND#3727;5:6.99466394187103:5.97069468343598e-05:0.00098324405872496!RFX5#5993;5:12.0479108271951:3.93714721313598e-06:0.00012742228626982!STAT3#6774;5:10.5194649971542:7.759040745861e-06:0.000220202841428526!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00917867716004474
|tf_chipseq_enrich=CEBPB#1051;5:7.97114762582482:3.10621793420244e-05:0.00062833680966525!EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00110693270718678!FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000388738853617863!GATA2#2624;5:12.744931733554:2.9719152914525e-06:0.000101102234893814!JUN#3725;5:12.5128291923363:3.25800591331781e-06:0.00010902367176578!JUND#3727;5:6.99466394187103:5.97069468343598e-05:0.00098324405872496!RFX5#5993;5:12.0479108271951:3.93714721313598e-06:0.00012742228626982!STAT3#6774;5:10.5194649971542:7.759040745861e-06:0.000220202841428526!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00917867716004474
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}}
}}

Revision as of 15:01, 26 November 2012


Full id: C1655_large_mesothelioma_Fibroblast_giant_oral_mesenchymal_mucinous



Phase1 CAGE Peaks

Hg19::chr12:104674502..104674520,-p5@ENST00000549807
Hg19::chr12:104674521..104674536,-p4@ENST00000549807
Hg19::chr12:104674543..104674573,-p2@ENST00000549807
Hg19::chr12:104674575..104674595,-p3@ENST00000549807
Hg19::chr12:104674604..104674628,-p1@ENST00000549807


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 GOStat results

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
mesothelial cell6.03e-1619
mesodermal cell7.37e-16121
squamous epithelial cell8.68e-1563
animal cell9.36e-14679
eukaryotic cell9.36e-14679
lining cell2.96e-1358
barrier cell2.96e-1358
epithelial cell1.37e-10253
embryonic cell3.39e-10250
fibroblast4.24e-1076
native cell2.40e-09722
Uber Anatomy
Ontology termp-valuen
vasculature2.15e-0978
vascular system2.15e-0978
vessel6.72e-0968
splanchnic layer of lateral plate mesoderm6.13e-0883
epithelial tube open at both ends9.66e-0859
blood vessel9.66e-0859
blood vasculature9.66e-0859
vascular cord9.66e-0859
epithelial tube1.26e-07117
aorta1.55e-0721
aortic system1.55e-0721
cardiovascular system1.58e-07109
artery1.99e-0742
arterial blood vessel1.99e-0742
arterial system1.99e-0742
unilaminar epithelium2.28e-07148
circulatory system5.34e-07112
larynx7.33e-079
systemic artery9.97e-0733
systemic arterial system9.97e-0733
Disease
Ontology termp-valuen
disease of cellular proliferation3.86e-09239
cancer1.05e-07235
carcinoma2.65e-07106
cell type cancer8.45e-07143


Overrepresented TFBS (DNA) motifs on this co-expression cluster<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}}}



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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CEBPB#105157.971147625824823.10621793420244e-050.00062833680966525
EP300#203356.77394172622327.00901578206049e-050.00110693270718678
FOS#235358.99795530889441.69470025615156e-050.000388738853617863
GATA2#2624512.7449317335542.9719152914525e-060.000101102234893814
JUN#3725512.51282919233633.25800591331781e-060.00010902367176578
JUND#372756.994663941871035.97069468343598e-050.00098324405872496
RFX5#5993512.04791082719513.93714721313598e-060.00012742228626982
STAT3#6774510.51946499715427.759040745861e-060.000220202841428526
TBP#690853.706770687096390.001428755106721120.00917867716004474



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

This analysis result is provided for C0 - C305 clusters.

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