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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3024_Fibroblast_lung_Wilms_Adipocyte_Cardiac_aorta_heart
|full_id=C3024_Fibroblast_lung_Wilms_Adipocyte_Cardiac_aorta_heart
|id=C3024
|id=C3024

Revision as of 15:52, 12 September 2012


Full id: C3024_Fibroblast_lung_Wilms_Adipocyte_Cardiac_aorta_heart



Phase1 CAGE Peaks

Hg19::chr10:52750837..52750889,+p4@PRKG1
Hg19::chr10:52750899..52750917,+p6@PRKG1
Hg19::chr10:52750930..52750950,+p5@PRKG1


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
muscle tissue4.90e-1863
musculature4.90e-1863
musculature of body4.90e-1863
skeletal muscle tissue1.53e-1761
striated muscle tissue1.53e-1761
myotome1.53e-1761
dermomyotome2.27e-1770
adult organism2.66e-16115
organism subdivision9.72e-16365
somite1.41e-1583
paraxial mesoderm1.41e-1583
presomitic mesoderm1.41e-1583
presumptive segmental plate1.41e-1583
trunk paraxial mesoderm1.41e-1583
presumptive paraxial mesoderm1.41e-1583
primary circulatory organ2.05e-1427
multilaminar epithelium9.21e-1382
heart1.12e-1224
primitive heart tube1.12e-1224
primary heart field1.12e-1224
anterior lateral plate mesoderm1.12e-1224
heart tube1.12e-1224
heart primordium1.12e-1224
cardiac mesoderm1.12e-1224
cardiogenic plate1.12e-1224
heart rudiment1.12e-1224
multi-tissue structure1.35e-12347
splanchnic layer of lateral plate mesoderm3.25e-1284
epithelium2.35e-11309
cell layer5.76e-11312
trunk mesenchyme2.92e-10143
multi-cellular organism3.05e-10659
trunk1.64e-09216
tube5.35e-09194
anatomical conduit1.50e-08241
anatomical cluster3.04e-08286
unilaminar epithelium3.92e-08138
circulatory system1.48e-07113
compound organ4.26e-0769
anatomical system6.09e-07625
artery6.32e-0742
arterial blood vessel6.32e-0742
arterial system6.32e-0742
epithelial tube6.56e-07118
blood vessel8.07e-0760
epithelial tube open at both ends8.07e-0760
blood vasculature8.07e-0760
vascular cord8.07e-0760
anatomical group8.29e-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
USF1#739136.361499277207960.00388404057290560.0189429958622251



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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