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Coexpression cluster:C2581: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2581_Renal_Endothelial_extraskeletal_Hepatic_Lymphatic_Mesenchymal_Smooth
|full_id=C2581_Renal_Endothelial_extraskeletal_Hepatic_Lymphatic_Mesenchymal_Smooth
|id=C2581
|id=C2581

Revision as of 15:20, 12 September 2012


Full id: C2581_Renal_Endothelial_extraskeletal_Hepatic_Lymphatic_Mesenchymal_Smooth



Phase1 CAGE Peaks

Hg19::chr1:32538492..32538508,+p2@TMEM39B
Hg19::chr4:145567043..145567058,-p3@ENST00000503066
Hg19::chr4:145567059..145567099,-p1@ENST00000503066
Hg19::chr4:145567114..145567191,-p1@LOC646576


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><br>

Uber Anatomy
Ontology termp-valuen
vasculature3.58e-3579
vascular system3.58e-3579
vessel1.64e-3069
anatomical cluster1.21e-29286
cell layer6.95e-29312
tube3.60e-28194
blood vessel1.23e-2760
epithelial tube open at both ends1.23e-2760
blood vasculature1.23e-2760
vascular cord1.23e-2760
epithelium1.42e-27309
splanchnic layer of lateral plate mesoderm2.98e-2784
anatomical conduit9.07e-27241
cardiovascular system3.22e-26110
epithelial tube5.16e-26118
circulatory system2.02e-24113
artery9.17e-2242
arterial blood vessel9.17e-2242
arterial system9.17e-2242
unilaminar epithelium2.60e-20138
multi-tissue structure1.56e-17347
systemic artery9.89e-1733
systemic arterial system9.89e-1733
muscle tissue3.95e-1663
musculature3.95e-1663
musculature of body3.95e-1663
skeletal muscle tissue4.17e-1661
striated muscle tissue4.17e-1661
myotome4.17e-1661
dermomyotome1.29e-1570
somite1.80e-1483
paraxial mesoderm1.80e-1483
presomitic mesoderm1.80e-1483
presumptive segmental plate1.80e-1483
trunk paraxial mesoderm1.80e-1483
presumptive paraxial mesoderm1.80e-1483
trunk mesenchyme4.33e-14143
organism subdivision2.69e-13365
endothelium3.57e-1318
blood vessel endothelium3.57e-1318
cardiovascular system endothelium3.57e-1318
multilaminar epithelium2.54e-1282
squamous epithelium9.37e-1225
simple squamous epithelium2.22e-1122
aorta1.21e-1021
aortic system1.21e-1021
trunk3.66e-09216
mesenchyme4.38e-09238
entire embryonic mesenchyme4.38e-09238
multi-cellular organism4.02e-08659
endothelial tube2.09e-079
arterial system endothelium2.09e-079
endothelium of artery2.09e-079
embryo2.58e-07612
compound organ4.66e-0769
embryonic structure5.76e-07605
developing anatomical structure5.76e-07605
anatomical system6.06e-07625
germ layer8.20e-07604
embryonic tissue8.20e-07604
presumptive structure8.20e-07604
epiblast (generic)8.20e-07604
anatomical group8.28e-07626


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
EBF1#187936.679850134926750.005184294118278910.0240502151387612
FOS#235348.99795530889440.0001525147711168630.00195034776303099



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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