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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1982_Fibroblast_Mesenchymal_tenocyte_Hair_normal_Synoviocyte_mesenchymal
|full_id=C1982_Fibroblast_Mesenchymal_tenocyte_Hair_normal_Synoviocyte_mesenchymal
|gostat_on_coexpression_clusters=GO:0005518!collagen binding!0.00279642058165548!5118
|gostat_on_coexpression_clusters=GO:0005518!collagen binding!0.00279642058165548!5118

Revision as of 14:37, 12 September 2012


Full id: C1982_Fibroblast_Mesenchymal_tenocyte_Hair_normal_Synoviocyte_mesenchymal



Phase1 CAGE Peaks

Hg19::chr7:100201080..100201091,+p12@PCOLCE
Hg19::chr7:100201103..100201120,+p3@PCOLCE
Hg19::chr7:100201144..100201162,-p1@ENST00000544873
Hg19::chr7:100202784..100202796,-p@chr7:100202784..100202796
-
Hg19::chr7:100203376..100203387,+p15@PCOLCE


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

GO IDGO nameFDR corrected p-value
GO:0005518collagen binding0.00279642058165548



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
somite1.12e-2683
paraxial mesoderm1.12e-2683
presomitic mesoderm1.12e-2683
presumptive segmental plate1.12e-2683
trunk paraxial mesoderm1.12e-2683
presumptive paraxial mesoderm1.12e-2683
dermomyotome4.19e-2470
skeletal muscle tissue2.39e-2061
striated muscle tissue2.39e-2061
myotome2.39e-2061
muscle tissue2.99e-2063
musculature2.99e-2063
musculature of body2.99e-2063
multilaminar epithelium2.71e-1982
trunk mesenchyme1.30e-16143
organism subdivision1.03e-11365
surface structure1.77e-1195
integument1.33e-1045
integumental system1.33e-1045
trunk1.29e-09216
multi-tissue structure1.46e-08347
skin of body1.96e-0840
splanchnic layer of lateral plate mesoderm2.40e-0884
adipose tissue3.14e-0814
multi-cellular organism7.77e-08659
heart8.57e-0824
primitive heart tube8.57e-0824
primary heart field8.57e-0824
anterior lateral plate mesoderm8.57e-0824
heart tube8.57e-0824
heart primordium8.57e-0824
cardiac mesoderm8.57e-0824
cardiogenic plate8.57e-0824
heart rudiment8.57e-0824
primary circulatory organ1.17e-0727
mesenchyme1.23e-07238
entire embryonic mesenchyme1.23e-07238
tissue4.63e-07787
unilaminar epithelium5.82e-07138


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

No analysis results for this cluster

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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