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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2582_Renal_Melanocyte_vagina_Hepatic_Endothelial_lung_Hepatocyte
|full_id=C2582_Renal_Melanocyte_vagina_Hepatic_Endothelial_lung_Hepatocyte
|id=C2582
|id=C2582

Revision as of 15:20, 12 September 2012


Full id: C2582_Renal_Melanocyte_vagina_Hepatic_Endothelial_lung_Hepatocyte



Phase1 CAGE Peaks

Hg19::chr1:32712815..32712842,+p1@FAM167B
Hg19::chr1:32712845..32712856,+p2@FAM167B
Hg19::chr1:32712858..32712867,+p4@FAM167B
Hg19::chr1:32712897..32712909,+p3@FAM167B


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
anatomical cluster5.01e-23286
adult organism1.18e-18115
anatomical conduit1.58e-18241
splanchnic layer of lateral plate mesoderm1.92e-1784
vessel3.29e-1669
tube4.92e-16194
epithelial tube3.18e-15118
blood vessel4.16e-1460
epithelial tube open at both ends4.16e-1460
blood vasculature4.16e-1460
vascular cord4.16e-1460
vasculature1.14e-1279
vascular system1.14e-1279
circulatory system1.22e-11113
cardiovascular system8.84e-11110
epithelium8.94e-11309
anatomical system9.57e-11625
anatomical group1.43e-10626
multi-tissue structure2.12e-10347
cell layer3.45e-10312
multi-cellular organism3.79e-10659
artery1.50e-0942
arterial blood vessel1.50e-0942
arterial system1.50e-0942
primary circulatory organ5.77e-0927
systemic artery3.63e-0833
systemic arterial system3.63e-0833
heart6.41e-0824
primitive heart tube6.41e-0824
primary heart field6.41e-0824
anterior lateral plate mesoderm6.41e-0824
heart tube6.41e-0824
heart primordium6.41e-0824
cardiac mesoderm6.41e-0824
cardiogenic plate6.41e-0824
heart rudiment6.41e-0824
organism subdivision2.06e-07365
unilaminar epithelium2.87e-07138
larynx5.82e-079
endothelium7.47e-0718
blood vessel endothelium7.47e-0718
cardiovascular system endothelium7.47e-0718


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
STAT1#6772420.70658749719925.43610708103893e-060.000165425870465217
STAT3#6774410.51946499715428.16377768286615e-050.00123210516968332
USF1#739146.361499277207960.0006105011399140830.00508251323646767



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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