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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4809_Pericytes_Mesenchymal_Fibroblast_Smooth_Chondrocyte_Preadipocyte_Lens
|full_id=C4809_Pericytes_Mesenchymal_Fibroblast_Smooth_Chondrocyte_Preadipocyte_Lens
|id=C4809
|id=C4809

Revision as of 17:57, 12 September 2012


Full id: C4809_Pericytes_Mesenchymal_Fibroblast_Smooth_Chondrocyte_Preadipocyte_Lens



Phase1 CAGE Peaks

Hg19::chr9:137533542..137533553,+p6@COL5A1
Hg19::chr9:137533569..137533580,+p3@COL5A1
Hg19::chr9:137533862..137533873,+p9@COL5A1


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
splanchnic layer of lateral plate mesoderm9.60e-1284
vasculature2.48e-1179
vascular system2.48e-1179
somite4.22e-1083
paraxial mesoderm4.22e-1083
presomitic mesoderm4.22e-1083
presumptive segmental plate4.22e-1083
trunk paraxial mesoderm4.22e-1083
presumptive paraxial mesoderm4.22e-1083
skeletal muscle tissue7.98e-1061
striated muscle tissue7.98e-1061
myotome7.98e-1061
dermomyotome1.51e-0970
muscle tissue2.05e-0963
musculature2.05e-0963
musculature of body2.05e-0963
extraembryonic structure2.71e-0824
multi-cellular organism4.77e-08659
cardiovascular system5.32e-08110
multilaminar epithelium7.07e-0882
blood vessel9.86e-0860
epithelial tube open at both ends9.86e-0860
blood vasculature9.86e-0860
vascular cord9.86e-0860
epithelial tube1.68e-07118
trunk mesenchyme1.88e-07143
extraembryonic membrane1.98e-0714
membranous layer1.98e-0714
circulatory system2.72e-07113
vessel3.08e-0769
unilaminar epithelium5.63e-07138
organ component layer7.15e-0757


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
SP1#666735.69838137814090.005403962701712170.0248135616884641
ZNF263#1012738.221841637010680.001799043925565870.0110251348751423



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.