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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C907_Adipocyte_aorta_Smooth_Hepatic_Fibroblast_spleen_Mesenchymal
|full_id=C907_Adipocyte_aorta_Smooth_Hepatic_Fibroblast_spleen_Mesenchymal
|id=C907
|id=C907

Revision as of 18:41, 12 September 2012


Full id: C907_Adipocyte_aorta_Smooth_Hepatic_Fibroblast_spleen_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr14:92413867..92413880,-p11@FBLN5
Hg19::chr14:92413889..92413894,-p19@FBLN5
Hg19::chr14:92413896..92413917,-p10@FBLN5
Hg19::chr14:92413918..92413933,-p5@FBLN5
Hg19::chr14:92413955..92413970,-p6@FBLN5
Hg19::chr14:92413978..92413995,-p8@FBLN5
Hg19::chr14:92413998..92414054,-p3@FBLN5
Hg19::chr14:92414055..92414065,-p15@FBLN5
Hg19::chr14:92414271..92414293,-p21@FBLN5


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
organism subdivision9.25e-20365
multi-tissue structure1.79e-18347
multi-cellular organism4.22e-18659
somite3.50e-1683
paraxial mesoderm3.50e-1683
presomitic mesoderm3.50e-1683
presumptive segmental plate3.50e-1683
trunk paraxial mesoderm3.50e-1683
presumptive paraxial mesoderm3.50e-1683
dermomyotome8.70e-1670
adult organism1.74e-15115
muscle tissue1.04e-1463
musculature1.04e-1463
musculature of body1.04e-1463
skeletal muscle tissue5.52e-1461
striated muscle tissue5.52e-1461
myotome5.52e-1461
anatomical system6.36e-14625
cell layer1.18e-13312
anatomical group1.26e-13626
anatomical cluster3.75e-13286
trunk mesenchyme3.75e-13143
epithelium4.65e-13309
multilaminar epithelium1.21e-1282
trunk1.82e-11216
embryo1.22e-10612
embryonic structure1.49e-10605
developing anatomical structure1.49e-10605
germ layer2.97e-10604
embryonic tissue2.97e-10604
presumptive structure2.97e-10604
epiblast (generic)2.97e-10604
mesenchyme4.21e-10238
entire embryonic mesenchyme4.21e-10238
anatomical conduit6.35e-10241
splanchnic layer of lateral plate mesoderm4.12e-0984
organ1.02e-08511
primary circulatory organ1.60e-0827
tube1.55e-07194
tissue2.87e-07787
surface structure3.08e-0795
adipose tissue3.69e-0714
heart4.07e-0724
primitive heart tube4.07e-0724
primary heart field4.07e-0724
anterior lateral plate mesoderm4.07e-0724
heart tube4.07e-0724
heart primordium4.07e-0724
cardiac mesoderm4.07e-0724
cardiogenic plate4.07e-0724
heart rudiment4.07e-0724
unilaminar epithelium4.45e-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
E2F1#186984.36212374655942.18983367577486e-050.000481077070391777
POLR2A#543081.908847268051620.0116612289598830.0425834647322104
STAT1#677236.902195832399730.007591561082166650.0312886759218786



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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