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Coexpression cluster:C4287: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.011552760792698!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280403264349406!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326542570001232!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00917590651342515!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248871122124362!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00617350179664811!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197573103265707
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.011552760792698!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280403264349406!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326542570001232!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00917590651342515!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248871122124362!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00617350179664811!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197573103265707
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}}
}}

Revision as of 16:39, 26 November 2012


Full id: C4287_Mast_Pancreatic_Prostate_Fibroblast_Hair_Olfactory_schwannoma



Phase1 CAGE Peaks

Hg19::chr3:141121820..141121838,+p9@ZBTB38
Hg19::chr3:141121847..141121868,+p5@ZBTB38
Hg19::chr3:141121871..141121885,+p13@ZBTB38


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>


Uber Anatomy
Ontology termp-valuen
somite8.02e-1771
presomitic mesoderm8.02e-1771
presumptive segmental plate8.02e-1771
dermomyotome8.02e-1771
trunk paraxial mesoderm8.02e-1771
dense mesenchyme tissue2.15e-1673
paraxial mesoderm2.90e-1672
presumptive paraxial mesoderm2.90e-1672
surface structure1.18e-1599
multilaminar epithelium2.18e-1583
epithelial vesicle5.11e-1478
muscle tissue2.12e-1264
musculature2.12e-1264
musculature of body2.12e-1264
skeletal muscle tissue3.67e-1262
striated muscle tissue3.67e-1262
myotome3.67e-1262
skin of body3.02e-1141
integument3.18e-1046
integumental system3.18e-1046
trunk mesenchyme7.15e-10122
organism subdivision6.70e-09264
multi-tissue structure1.91e-07342
mesenchyme2.89e-07160
entire embryonic mesenchyme2.89e-07160
dermis4.69e-079
dermatome4.69e-079
future dermis4.69e-079
gingiva5.12e-078
unilaminar epithelium7.55e-07148
systemic artery9.44e-0733
systemic arterial system9.44e-0733
Disease
Ontology termp-valuen
ovarian cancer5.18e-0814


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)

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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#105137.971147625824820.001974187055288560.011552760792698
CTCF#1066435.360256373075030.0064925092527670.0280403264349406
E2F1#186934.907389214879320.008460985347239390.0326542570001232
EBF1#187938.9064668465690.00141523283560980.00917590651342515
TFAP2A#7020316.5186343730450.0002218033880766340.00248871122124362
TFAP2C#7022310.80922860986020.0007916746575753130.00617350179664811
TRIM28#10155318.59052504526250.0001555969297255280.00197573103265707



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.