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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3362_Mesenchymal_Smooth_mesenchymal_Mesothelial_Aortic_Endothelial_Preadipocyte
|full_id=C3362_Mesenchymal_Smooth_mesenchymal_Mesothelial_Aortic_Endothelial_Preadipocyte
|id=C3362
|id=C3362

Revision as of 16:16, 12 September 2012


Full id: C3362_Mesenchymal_Smooth_mesenchymal_Mesothelial_Aortic_Endothelial_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr13:28896641..28896653,-p5@FLT1
Hg19::chr4:120446538..120446544,-p@chr4:120446538..120446544
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Hg19::chr9:93271212..93271237,-p@chr9:93271212..93271237
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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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
artery5.68e-1642
arterial blood vessel5.68e-1642
arterial system5.68e-1642
vessel2.35e-1269
vasculature2.40e-1279
vascular system2.40e-1279
umbilical artery4.42e-114
blood vessel8.03e-1160
epithelial tube open at both ends8.03e-1160
blood vasculature8.03e-1160
vascular cord8.03e-1160
unilaminar epithelium2.34e-10138
skeletal muscle tissue2.84e-1061
striated muscle tissue2.84e-1061
myotome2.84e-1061
muscle tissue8.73e-1063
musculature8.73e-1063
musculature of body8.73e-1063
cardiovascular system1.99e-09110
circulatory system5.43e-09113
splanchnic layer of lateral plate mesoderm7.78e-0984
dermomyotome2.61e-0870
epithelial tube2.84e-08118
right ovary5.37e-085
systemic artery6.27e-0833
systemic arterial system6.27e-0833
smooth muscle tissue7.00e-0715
Disease
Ontology termp-valuen
ovarian cancer4.28e-1614
reproductive organ cancer5.07e-0829
female reproductive organ cancer3.07e-0727


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.