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Coexpression cluster:C3336: Difference between revisions

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|ontology_enrichment_disease=DOID:305!3.25e-12!106;DOID:0050687!7.25e-12!143;DOID:162!6.21e-08!235;DOID:14566!1.09e-07!239
|ontology_enrichment_disease=DOID:305!3.25e-12!106;DOID:0050687!7.25e-12!143;DOID:162!6.21e-08!235;DOID:14566!1.09e-07!239
|ontology_enrichment_uberon=UBERON:0009569!4.88e-11!113;UBERON:0003914!5.76e-11!118;UBERON:0003886!7.64e-11!63;UBERON:0000466!5.29e-10!126;UBERON:0002553!5.35e-10!70;UBERON:0000487!1.60e-09!22;UBERON:0000464!1.74e-09!104;UBERON:0002417!7.38e-09!61;UBERON:0000916!7.38e-09!61;UBERON:0001986!7.55e-09!18;UBERON:0004638!7.55e-09!18;UBERON:0004852!7.55e-09!18;UBERON:0002049!1.09e-08!79;UBERON:0007798!1.09e-08!79;UBERON:0000058!6.46e-08!26;UBERON:0000477!1.07e-07!286;UBERON:0000055!1.78e-07!69;UBERON:0006914!2.11e-07!25;UBERON:0002113!2.22e-07!27;UBERON:0003918!2.22e-07!27;UBERON:0005095!2.22e-07!27;UBERON:0007687!2.22e-07!27;UBERON:0002100!2.41e-07!216;UBERON:0004876!5.44e-07!20;UBERON:0005172!7.94e-07!55;UBERON:0005173!7.94e-07!55;UBERON:0003064!8.38e-07!37;UBERON:0004211!9.93e-07!16;UBERON:0001285!9.93e-07!16;UBERON:0007684!9.93e-07!16;UBERON:0003220!9.93e-07!16;UBERON:0004208!9.93e-07!16
|ontology_enrichment_uberon=UBERON:0009569!4.88e-11!113;UBERON:0003914!5.76e-11!118;UBERON:0003886!7.64e-11!63;UBERON:0000466!5.29e-10!126;UBERON:0002553!5.35e-10!70;UBERON:0000487!1.60e-09!22;UBERON:0000464!1.74e-09!104;UBERON:0002417!7.38e-09!61;UBERON:0000916!7.38e-09!61;UBERON:0001986!7.55e-09!18;UBERON:0004638!7.55e-09!18;UBERON:0004852!7.55e-09!18;UBERON:0002049!1.09e-08!79;UBERON:0007798!1.09e-08!79;UBERON:0000058!6.46e-08!26;UBERON:0000477!1.07e-07!286;UBERON:0000055!1.78e-07!69;UBERON:0006914!2.11e-07!25;UBERON:0002113!2.22e-07!27;UBERON:0003918!2.22e-07!27;UBERON:0005095!2.22e-07!27;UBERON:0007687!2.22e-07!27;UBERON:0002100!2.41e-07!216;UBERON:0004876!5.44e-07!20;UBERON:0005172!7.94e-07!55;UBERON:0005173!7.94e-07!55;UBERON:0003064!8.38e-07!37;UBERON:0004211!9.93e-07!16;UBERON:0001285!9.93e-07!16;UBERON:0007684!9.93e-07!16;UBERON:0003220!9.93e-07!16;UBERON:0004208!9.93e-07!16
|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 13:35, 5 September 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 trunk4.88e-11113
epithelial tube5.76e-11118
body cavity precursor7.64e-1163
immaterial anatomical entity5.29e-10126
anatomical cavity5.35e-1070
simple squamous epithelium1.60e-0922
anatomical space1.74e-09104
abdominal segment of trunk7.38e-0961
abdomen7.38e-0961
endothelium7.55e-0918
blood vessel endothelium7.55e-0918
cardiovascular system endothelium7.55e-0918
vasculature1.09e-0879
vascular system1.09e-0879
duct6.46e-0826
anatomical cluster1.07e-07286
vessel1.78e-0769
squamous epithelium2.11e-0725
kidney2.22e-0727
kidney mesenchyme2.22e-0727
kidney rudiment2.22e-0727
kidney field2.22e-0727
trunk2.41e-07216
urogenital ridge5.44e-0720
abdomen element7.94e-0755
abdominal segment element7.94e-0755
intermediate mesoderm8.38e-0737
nephron epithelium9.93e-0716
nephron9.93e-0716
uriniferous tubule9.93e-0716
metanephric mesenchyme9.93e-0716
nephrogenic mesenchyme9.93e-0716
Disease
Ontology termp-valuen
carcinoma3.25e-12106
cell type cancer7.25e-12143
cancer6.21e-08235
disease of cellular proliferation1.09e-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)

{{{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
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.