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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3522_Fibroblast_Smooth_basal_mesenchymal_Meningeal_Ewing_Preadipocyte
|full_id=C3522_Fibroblast_Smooth_basal_mesenchymal_Meningeal_Ewing_Preadipocyte
|id=C3522
|id=C3522

Revision as of 16:27, 12 September 2012


Full id: C3522_Fibroblast_Smooth_basal_mesenchymal_Meningeal_Ewing_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr15:80842610..80842647,-p@chr15:80842610..80842647
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Hg19::chr15:80842672..80842689,-p@chr15:80842672..80842689
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Hg19::chr15:80842696..80842711,-p@chr15:80842696..80842711
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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
dermomyotome1.06e-2470
somite1.29e-2483
paraxial mesoderm1.29e-2483
presomitic mesoderm1.29e-2483
presumptive segmental plate1.29e-2483
trunk paraxial mesoderm1.29e-2483
presumptive paraxial mesoderm1.29e-2483
skeletal muscle tissue4.78e-2261
striated muscle tissue4.78e-2261
myotome4.78e-2261
muscle tissue9.28e-2163
musculature9.28e-2163
musculature of body9.28e-2163
multilaminar epithelium8.41e-2082
organism subdivision2.19e-18365
trunk mesenchyme4.39e-16143
cell layer1.15e-12312
artery2.33e-1242
arterial blood vessel2.33e-1242
arterial system2.33e-1242
trunk1.95e-11216
epithelium2.07e-11309
splanchnic layer of lateral plate mesoderm2.81e-1184
systemic artery9.32e-1133
systemic arterial system9.32e-1133
skin of body3.99e-1040
unilaminar epithelium6.12e-10138
vasculature1.16e-0979
vascular system1.16e-0979
cardiovascular system1.40e-09110
integument1.61e-0945
integumental system1.61e-0945
circulatory system6.76e-09113
tube1.28e-08194
epithelial tube1.79e-08118
blood vessel2.61e-0860
epithelial tube open at both ends2.61e-0860
blood vasculature2.61e-0860
vascular cord2.61e-0860
anatomical cluster4.52e-08286
heart7.31e-0824
primitive heart tube7.31e-0824
primary heart field7.31e-0824
anterior lateral plate mesoderm7.31e-0824
heart tube7.31e-0824
heart primordium7.31e-0824
cardiac mesoderm7.31e-0824
cardiogenic plate7.31e-0824
heart rudiment7.31e-0824
multi-tissue structure8.69e-08347
vessel3.79e-0769
surface structure4.68e-0795
anatomical conduit5.35e-07241


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
EP300#203336.77394172622320.003216880500103790.0167256326255957



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.