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Coexpression cluster:C2697: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2697_Chondrocyte_mesenchymal_Fibroblast_Smooth_Anulus_hepatic_aorta
|full_id=C2697_Chondrocyte_mesenchymal_Fibroblast_Smooth_Anulus_hepatic_aorta
|id=C2697
|id=C2697

Revision as of 15:27, 12 September 2012


Full id: C2697_Chondrocyte_mesenchymal_Fibroblast_Smooth_Anulus_hepatic_aorta



Phase1 CAGE Peaks

Hg19::chr2:33359579..33359590,+p4@LTBP1
Hg19::chr2:33359634..33359645,+p5@LTBP1
Hg19::chr2:33359646..33359686,+p1@LTBP1
Hg19::chr2:33359687..33359717,+p2@LTBP1


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
somite1.57e-3083
paraxial mesoderm1.57e-3083
presomitic mesoderm1.57e-3083
presumptive segmental plate1.57e-3083
trunk paraxial mesoderm1.57e-3083
presumptive paraxial mesoderm1.57e-3083
dermomyotome3.20e-2670
muscle tissue4.61e-2263
musculature4.61e-2263
musculature of body4.61e-2263
skeletal muscle tissue7.80e-2261
striated muscle tissue7.80e-2261
myotome7.80e-2261
organism subdivision3.78e-21365
multilaminar epithelium1.75e-2082
circulatory system4.56e-20113
cardiovascular system1.14e-19110
trunk mesenchyme1.43e-19143
multi-tissue structure1.31e-17347
splanchnic layer of lateral plate mesoderm5.39e-1784
multi-cellular organism7.13e-17659
cell layer1.30e-16312
artery1.98e-1642
arterial blood vessel1.98e-1642
arterial system1.98e-1642
vasculature2.50e-1679
vascular system2.50e-1679
epithelium1.22e-15309
systemic artery1.71e-1433
systemic arterial system1.71e-1433
anatomical system5.31e-14625
blood vessel5.89e-1460
epithelial tube open at both ends5.89e-1460
blood vasculature5.89e-1460
vascular cord5.89e-1460
anatomical group1.03e-13626
vessel2.00e-1369
surface structure2.39e-1395
anatomical cluster3.64e-12286
trunk7.59e-12216
unilaminar epithelium8.69e-12138
anatomical conduit2.82e-11241
epithelial tube3.87e-11118
embryonic structure3.30e-10605
developing anatomical structure3.30e-10605
tissue3.63e-10787
germ layer4.27e-10604
embryonic tissue4.27e-10604
presumptive structure4.27e-10604
epiblast (generic)4.27e-10604
mesenchyme6.43e-10238
entire embryonic mesenchyme6.43e-10238
embryo8.21e-10612
integument3.35e-0945
integumental system3.35e-0945
primary circulatory organ6.44e-0927
tube7.66e-09194
heart1.04e-0824
primitive heart tube1.04e-0824
primary heart field1.04e-0824
anterior lateral plate mesoderm1.04e-0824
heart tube1.04e-0824
heart primordium1.04e-0824
cardiac mesoderm1.04e-0824
cardiogenic plate1.04e-0824
heart rudiment1.04e-0824
aorta1.62e-0821
aortic system1.62e-0821
skin of body4.14e-0840
adult organism1.72e-07115
smooth muscle tissue9.70e-0715


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
CTCF#1066445.360256373075030.001211145381643620.00818657773046911
EP300#203346.77394172622320.0004748459821442640.00434678232353097
NR3C1#2908414.9730233311731.98868032687801e-050.000443699604056425
RAD21#5885410.35503389545638.6948481184721e-050.00129688837852772
STAT3#6774410.51946499715428.16377768286615e-050.00123317439603827



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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