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Coexpression cluster:C3336: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278709019626673!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00913168800928286!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460703964343273!MYC#4609;3:5.2222818716094:0.00702084375574015:0.029360530992462!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00662531885911306!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328410189772067
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278709019626673!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00913168800928286!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460703964343273!MYC#4609;3:5.2222818716094:0.00702084375574015:0.029360530992462!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00662531885911306!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328410189772067
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}}
}}

Revision as of 16:04, 26 November 2012


Full id: C3336_mesothelioma_testicular_extraskeletal_Endothelial_Lens_pancreatic_Renal



Phase1 CAGE Peaks

Hg19::chr12:80084120..80084136,-p15@PAWR
Hg19::chr12:80084137..80084165,-p10@PAWR
Hg19::chr12:80084167..80084197,-p5@PAWR


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
subdivision of trunk7.28e-11112
epithelial tube1.56e-10117
abdominal segment of trunk2.36e-0960
abdomen2.36e-0960
simple squamous epithelium3.63e-0922
anatomical cluster6.74e-09373
blood vessel endothelium8.26e-0918
endothelium8.26e-0918
cardiovascular system endothelium8.26e-0918
vasculature1.35e-0878
vascular system1.35e-0878
body cavity precursor1.22e-0754
immaterial anatomical entity2.35e-07117
kidney2.60e-0726
kidney mesenchyme2.60e-0726
upper urinary tract2.60e-0726
kidney rudiment2.60e-0726
kidney field2.60e-0726
squamous epithelium2.78e-0725
organism subdivision2.79e-07264
nephron epithelium2.89e-0715
renal tubule2.89e-0715
nephron tubule2.89e-0715
nephron2.89e-0715
uriniferous tubule2.89e-0715
nephrogenic mesenchyme2.89e-0715
abdomen element3.32e-0754
abdominal segment element3.32e-0754
cortex3.90e-0715
vessel4.34e-0768
anatomical cavity7.46e-0761
trunk region element8.77e-07101
Disease
Ontology termp-valuen
cell type cancer5.31e-11143
carcinoma5.58e-11106
cancer3.10e-07235
disease of cellular proliferation3.71e-07239


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
CTCF#1066435.360256373075030.0064925092527670.0278709019626673
EBF1#187938.9064668465690.00141523283560980.00913168800928286
ELF1#199734.258097958807540.01295179875054610.0460703964343273
MYC#460935.22228187160940.007020843755740150.029360530992462
RAD21#5885310.35503389545630.0009004912073565420.00662531885911306
YY1#752834.911170749853860.008441455341808260.0328410189772067



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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