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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4546_mature_Adipocyte_Fibroblast_mesenchymal_vagina_Smooth_normal
|full_id=C4546_mature_Adipocyte_Fibroblast_mesenchymal_vagina_Smooth_normal
|id=C4546
|id=C4546

Revision as of 17:38, 12 September 2012


Full id: C4546_mature_Adipocyte_Fibroblast_mesenchymal_vagina_Smooth_normal



Phase1 CAGE Peaks

Hg19::chr6:112575395..112575422,-p7@LAMA4
Hg19::chr6:112575434..112575448,-p9@LAMA4
Hg19::chr6:112575456..112575485,-p5@LAMA4


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
vasculature1.14e-1479
vascular system1.14e-1479
organism subdivision1.09e-12365
somite1.79e-1283
paraxial mesoderm1.79e-1283
presomitic mesoderm1.79e-1283
presumptive segmental plate1.79e-1283
trunk paraxial mesoderm1.79e-1283
presumptive paraxial mesoderm1.79e-1283
vessel4.78e-1269
dermomyotome1.76e-1170
circulatory system2.37e-11113
cardiovascular system3.98e-11110
muscle tissue1.57e-1063
musculature1.57e-1063
musculature of body1.57e-1063
anatomical cluster1.73e-10286
splanchnic layer of lateral plate mesoderm1.94e-1084
skeletal muscle tissue5.79e-1061
striated muscle tissue5.79e-1061
myotome5.79e-1061
blood vessel8.50e-1060
epithelial tube open at both ends8.50e-1060
blood vasculature8.50e-1060
vascular cord8.50e-1060
multi-cellular organism1.45e-09659
anatomical conduit2.22e-09241
multilaminar epithelium2.82e-0982
surface structure7.34e-0995
artery9.53e-0942
arterial blood vessel9.53e-0942
arterial system9.53e-0942
systemic artery9.90e-0933
systemic arterial system9.90e-0933
cell layer2.91e-08312
integument2.91e-0845
integumental system2.91e-0845
anatomical system3.54e-08625
anatomical group5.06e-08626
epithelium7.52e-08309
multi-tissue structure7.12e-07347
unilaminar epithelium8.10e-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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTBP2#1488362.71700033932814.049570681927e-060.000130414157400485
ZNF263#1012738.221841637010680.001799043925565870.0109986740351328



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.