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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3060_cord_glioblastoma_Fibroblast_adult_Hair_mesenchymal_Mesenchymal
|full_id=C3060_cord_glioblastoma_Fibroblast_adult_Hair_mesenchymal_Mesenchymal
|id=C3060
|id=C3060

Revision as of 15:55, 12 September 2012


Full id: C3060_cord_glioblastoma_Fibroblast_adult_Hair_mesenchymal_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr10:95139640..95139659,-p@chr10:95139640..95139659
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Hg19::chr10:95139664..95139690,-p@chr10:95139664..95139690
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Hg19::chr10:95139698..95139709,-p@chr10:95139698..95139709
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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
somite1.30e-1283
paraxial mesoderm1.30e-1283
presomitic mesoderm1.30e-1283
presumptive segmental plate1.30e-1283
trunk paraxial mesoderm1.30e-1283
presumptive paraxial mesoderm1.30e-1283
multilaminar epithelium1.17e-1082
dermomyotome1.74e-1070
vasculature5.22e-1079
vascular system5.22e-1079
integument5.73e-0945
integumental system5.73e-0945
surface structure1.12e-0895
skeletal muscle tissue1.44e-0861
striated muscle tissue1.44e-0861
myotome1.44e-0861
skin of body2.30e-0840
blood vessel2.44e-0860
epithelial tube open at both ends2.44e-0860
blood vasculature2.44e-0860
vascular cord2.44e-0860
musculoskeletal system5.26e-08167
artery7.93e-0842
arterial blood vessel7.93e-0842
arterial system7.93e-0842
vessel8.10e-0869
muscle tissue9.69e-0863
musculature9.69e-0863
musculature of body9.69e-0863
trunk mesenchyme1.42e-07143
mesoderm2.46e-07448
mesoderm-derived structure2.46e-07448
presumptive mesoderm2.46e-07448


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
BATF#10538324.35780179230366.91705216281876e-050.00109855536927103
FOS#235338.99795530889440.001372499272417130.00894716007190391
JUN#3725312.51282919233630.0005103313992726250.00443046558675259



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.