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Coexpression cluster:C2058: Difference between revisions

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|ontology_enrichment_disease=DOID:2394!2.11e-08!14;DOID:120!8.57e-07!27;DOID:193!9.92e-07!29
|ontology_enrichment_disease=DOID:2394!2.11e-08!14;DOID:120!8.57e-07!27;DOID:193!9.92e-07!29
|ontology_enrichment_uberon=UBERON:0003914!2.20e-21!118;UBERON:0002100!4.96e-20!216;UBERON:0005256!6.78e-19!143;UBERON:0002049!1.06e-18!79;UBERON:0007798!1.06e-18!79;UBERON:0001637!2.73e-18!42;UBERON:0003509!2.73e-18!42;UBERON:0004572!2.73e-18!42;UBERON:0000490!1.01e-17!138;UBERON:0004872!1.47e-17!84;UBERON:0001981!2.24e-17!60;UBERON:0007500!2.24e-17!60;UBERON:0004537!2.24e-17!60;UBERON:0006965!2.24e-17!60;UBERON:0000486!4.27e-17!82;UBERON:0000914!9.69e-17!83;UBERON:0002329!9.69e-17!83;UBERON:0003077!9.69e-17!83;UBERON:0003059!9.69e-17!83;UBERON:0007282!9.69e-17!83;UBERON:0009618!9.69e-17!83;UBERON:0007285!9.69e-17!83;UBERON:0003104!1.54e-16!238;UBERON:0009142!1.54e-16!238;UBERON:0000926!1.64e-16!448;UBERON:0004120!1.64e-16!448;UBERON:0006603!1.64e-16!448;UBERON:0000055!1.78e-16!69;UBERON:0004573!8.33e-16!33;UBERON:0004571!8.33e-16!33;UBERON:0004290!4.59e-15!70;UBERON:0004535!3.99e-14!110;UBERON:0001009!1.98e-13!113;UBERON:0001134!2.25e-13!61;UBERON:0002036!2.25e-13!61;UBERON:0003082!2.25e-13!61;UBERON:0002385!7.33e-13!63;UBERON:0001015!7.33e-13!63;UBERON:0000383!7.33e-13!63;UBERON:0000467!4.98e-11!625;UBERON:0000480!8.42e-11!626;UBERON:0000468!1.19e-10!659;UBERON:0000947!2.94e-09!21;UBERON:0010191!2.94e-09!21;UBERON:0003102!5.28e-08!95;UBERON:0000475!2.60e-07!365;UBERON:0000481!5.80e-07!347;UBERON:0002199!8.94e-07!45;UBERON:0002416!8.94e-07!45;UBERON:0003886!9.20e-07!63
|ontology_enrichment_uberon=UBERON:0003914!2.20e-21!118;UBERON:0002100!4.96e-20!216;UBERON:0005256!6.78e-19!143;UBERON:0002049!1.06e-18!79;UBERON:0007798!1.06e-18!79;UBERON:0001637!2.73e-18!42;UBERON:0003509!2.73e-18!42;UBERON:0004572!2.73e-18!42;UBERON:0000490!1.01e-17!138;UBERON:0004872!1.47e-17!84;UBERON:0001981!2.24e-17!60;UBERON:0007500!2.24e-17!60;UBERON:0004537!2.24e-17!60;UBERON:0006965!2.24e-17!60;UBERON:0000486!4.27e-17!82;UBERON:0000914!9.69e-17!83;UBERON:0002329!9.69e-17!83;UBERON:0003077!9.69e-17!83;UBERON:0003059!9.69e-17!83;UBERON:0007282!9.69e-17!83;UBERON:0009618!9.69e-17!83;UBERON:0007285!9.69e-17!83;UBERON:0003104!1.54e-16!238;UBERON:0009142!1.54e-16!238;UBERON:0000926!1.64e-16!448;UBERON:0004120!1.64e-16!448;UBERON:0006603!1.64e-16!448;UBERON:0000055!1.78e-16!69;UBERON:0004573!8.33e-16!33;UBERON:0004571!8.33e-16!33;UBERON:0004290!4.59e-15!70;UBERON:0004535!3.99e-14!110;UBERON:0001009!1.98e-13!113;UBERON:0001134!2.25e-13!61;UBERON:0002036!2.25e-13!61;UBERON:0003082!2.25e-13!61;UBERON:0002385!7.33e-13!63;UBERON:0001015!7.33e-13!63;UBERON:0000383!7.33e-13!63;UBERON:0000467!4.98e-11!625;UBERON:0000480!8.42e-11!626;UBERON:0000468!1.19e-10!659;UBERON:0000947!2.94e-09!21;UBERON:0010191!2.94e-09!21;UBERON:0003102!5.28e-08!95;UBERON:0000475!2.60e-07!365;UBERON:0000481!5.80e-07!347;UBERON:0002199!8.94e-07!45;UBERON:0002416!8.94e-07!45;UBERON:0003886!9.20e-07!63
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}}
}}

Revision as of 13:36, 5 September 2012


Full id: C2058_Smooth_basal_mesenchymal_tubular_Renal_lung_Urothelial



Phase1 CAGE Peaks

Hg19::chr10:33246815..33246830,-p4@ITGB1
Hg19::chr10:33246846..33246855,-p11@ITGB1
Hg19::chr10:33246856..33246867,-p8@ITGB1
Hg19::chr10:33246874..33246907,-p2@ITGB1


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
epithelial tube2.20e-21118
trunk4.96e-20216
trunk mesenchyme6.78e-19143
vasculature1.06e-1879
vascular system1.06e-1879
artery2.73e-1842
arterial blood vessel2.73e-1842
arterial system2.73e-1842
unilaminar epithelium1.01e-17138
splanchnic layer of lateral plate mesoderm1.47e-1784
blood vessel2.24e-1760
epithelial tube open at both ends2.24e-1760
blood vasculature2.24e-1760
vascular cord2.24e-1760
multilaminar epithelium4.27e-1782
somite9.69e-1783
paraxial mesoderm9.69e-1783
presomitic mesoderm9.69e-1783
presumptive segmental plate9.69e-1783
trunk paraxial mesoderm9.69e-1783
presumptive paraxial mesoderm9.69e-1783
mesenchyme1.54e-16238
entire embryonic mesenchyme1.54e-16238
mesoderm1.64e-16448
mesoderm-derived structure1.64e-16448
presumptive mesoderm1.64e-16448
vessel1.78e-1669
systemic artery8.33e-1633
systemic arterial system8.33e-1633
dermomyotome4.59e-1570
cardiovascular system3.99e-14110
circulatory system1.98e-13113
skeletal muscle tissue2.25e-1361
striated muscle tissue2.25e-1361
myotome2.25e-1361
muscle tissue7.33e-1363
musculature7.33e-1363
musculature of body7.33e-1363
anatomical system4.98e-11625
anatomical group8.42e-11626
multi-cellular organism1.19e-10659
aorta2.94e-0921
aortic system2.94e-0921
surface structure5.28e-0895
organism subdivision2.60e-07365
multi-tissue structure5.80e-07347
integument8.94e-0745
integumental system8.94e-0745
body cavity precursor9.20e-0763
Disease
Ontology termp-valuen
ovarian cancer2.11e-0814
female reproductive organ cancer8.57e-0727
reproductive organ cancer9.92e-0729


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
CCNT2#90534.752151182721970.01386206996689490.0486995669157876
EGR1#195844.988179094810140.001615011500076050.0101218306562916
GABPB1#255347.067683836182170.0004006876864423170.00389604518055573
HEY1#2346244.040111043105710.00375304636917980.0185448717709486
HMGN3#932436.133910792512940.006640696683324720.0282849804612459
IRF1#365935.727872815172930.008097114790333330.0319814904919303
SIN3A#2594245.408884726815140.001168172384885160.00793978626220362
TAF1#687243.343046285745290.008005664898701650.0321084345758641
TAF7#6879411.43306940492395.85061525419808e-050.000966976430658638
ZBTB7A#5134147.35190930787590.000342223540015990.00345796094192434
ZEB1#6935312.66632401315790.000793336075912850.00612879846381109



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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