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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3694_Cardiac_Smooth_Mesenchymal_mesenchymal_Hair_heart_Fibroblast
|full_id=C3694_Cardiac_Smooth_Mesenchymal_mesenchymal_Hair_heart_Fibroblast
|id=C3694
|id=C3694

Revision as of 16:39, 12 September 2012


Full id: C3694_Cardiac_Smooth_Mesenchymal_mesenchymal_Hair_heart_Fibroblast



Phase1 CAGE Peaks

Hg19::chr17:77020146..77020158,+p7@C1QTNF1
Hg19::chr17:77020171..77020195,+p3@C1QTNF1
Hg19::chr17:77020477..77020492,+p6@C1QTNF1


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
somite1.39e-2683
paraxial mesoderm1.39e-2683
presomitic mesoderm1.39e-2683
presumptive segmental plate1.39e-2683
trunk paraxial mesoderm1.39e-2683
presumptive paraxial mesoderm1.39e-2683
multilaminar epithelium1.44e-2682
dermomyotome2.43e-2470
multi-tissue structure3.13e-23347
skeletal muscle tissue1.19e-2261
striated muscle tissue1.19e-2261
myotome1.19e-2261
muscle tissue2.83e-2263
musculature2.83e-2263
musculature of body2.83e-2263
trunk mesenchyme2.55e-21143
splanchnic layer of lateral plate mesoderm5.73e-2084
cell layer1.19e-19312
organism subdivision1.72e-19365
epithelium5.99e-19309
trunk1.65e-18216
circulatory system4.00e-18113
anatomical cluster3.92e-17286
mesenchyme8.32e-17238
entire embryonic mesenchyme8.32e-17238
cardiovascular system1.03e-16110
multi-cellular organism1.27e-16659
primary circulatory organ1.27e-1627
vasculature4.18e-1679
vascular system4.18e-1679
heart6.94e-1524
primitive heart tube6.94e-1524
primary heart field6.94e-1524
anterior lateral plate mesoderm6.94e-1524
heart tube6.94e-1524
heart primordium6.94e-1524
cardiac mesoderm6.94e-1524
cardiogenic plate6.94e-1524
heart rudiment6.94e-1524
epithelial tube1.70e-14118
vessel1.23e-1369
anatomical system1.23e-13625
anatomical group2.19e-13626
embryonic structure5.84e-13605
developing anatomical structure5.84e-13605
unilaminar epithelium6.25e-13138
germ layer6.32e-13604
embryonic tissue6.32e-13604
presumptive structure6.32e-13604
epiblast (generic)6.32e-13604
artery7.62e-1342
arterial blood vessel7.62e-1342
arterial system7.62e-1342
anatomical conduit7.96e-13241
systemic artery1.18e-1233
systemic arterial system1.18e-1233
blood vessel1.59e-1260
epithelial tube open at both ends1.59e-1260
blood vasculature1.59e-1260
vascular cord1.59e-1260
embryo2.64e-12612
compound organ1.53e-1169
primordium2.54e-10168
tube1.63e-08194
mesoderm2.31e-08448
mesoderm-derived structure2.31e-08448
presumptive mesoderm2.31e-08448
blood vessel smooth muscle3.96e-0710
arterial system smooth muscle3.96e-0710
artery smooth muscle tissue3.96e-0710
aorta smooth muscle tissue3.96e-0710
smooth muscle tissue4.28e-0715
Disease
Ontology termp-valuen
ovarian cancer7.35e-0814


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
ZNF263#1012738.221841637010680.001799043925565870.0109333924086223



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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