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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2017_Fibroblast_smooth_Smooth_bladder_hepatic_Cardiac_Mesenchymal
|full_id=C2017_Fibroblast_smooth_Smooth_bladder_hepatic_Cardiac_Mesenchymal
|id=C2017
|id=C2017

Revision as of 14:41, 12 September 2012


Full id: C2017_Fibroblast_smooth_Smooth_bladder_hepatic_Cardiac_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr9:125133293..125133309,+p2@PTGS1
Hg19::chr9:125133315..125133339,+p1@PTGS1
Hg19::chr9:125140209..125140236,+p@chr9:125140209..125140236
+
Hg19::chr9:125140793..125140811,+p@chr9:125140793..125140811
+
Hg19::chr9:125141103..125141134,-p@chr9:125141103..125141134
-


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
cardiovascular system4.77e-15110
circulatory system6.42e-15113
musculoskeletal system1.77e-14167
somite3.98e-1483
paraxial mesoderm3.98e-1483
presomitic mesoderm3.98e-1483
presumptive segmental plate3.98e-1483
trunk paraxial mesoderm3.98e-1483
presumptive paraxial mesoderm3.98e-1483
splanchnic layer of lateral plate mesoderm1.97e-1384
lateral plate mesoderm2.15e-13216
tissue2.39e-13787
dermomyotome3.95e-1370
muscle tissue2.86e-1163
musculature2.86e-1163
musculature of body2.86e-1163
mesoderm3.52e-11448
mesoderm-derived structure3.52e-11448
presumptive mesoderm3.52e-11448
artery9.58e-1142
arterial blood vessel9.58e-1142
arterial system9.58e-1142
connective tissue1.13e-10375
skeletal muscle tissue1.52e-1061
striated muscle tissue1.52e-1061
myotome1.52e-1061
multilaminar epithelium2.82e-1082
systemic artery4.71e-1033
systemic arterial system4.71e-1033
blood vessel3.94e-0960
epithelial tube open at both ends3.94e-0960
blood vasculature3.94e-0960
vascular cord3.94e-0960
heart7.20e-0924
primitive heart tube7.20e-0924
primary heart field7.20e-0924
anterior lateral plate mesoderm7.20e-0924
heart tube7.20e-0924
heart primordium7.20e-0924
cardiac mesoderm7.20e-0924
cardiogenic plate7.20e-0924
heart rudiment7.20e-0924
anatomical system1.07e-08625
anatomical group1.49e-08626
primary circulatory organ2.48e-0827
vessel2.51e-0869
multi-cellular organism4.22e-08659
vasculature7.29e-0879
vascular system7.29e-0879
trunk mesenchyme1.11e-07143
hemolymphoid system6.24e-07112
epithelial tube6.28e-07118
hematopoietic system7.35e-07102
blood island7.35e-07102


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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