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Coexpression cluster:C2442: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2442_Adipocyte_Cardiac_Mesenchymal_heart_mature_Hair_Smooth
|full_id=C2442_Adipocyte_Cardiac_Mesenchymal_heart_mature_Hair_Smooth
|id=C2442
|id=C2442

Revision as of 15:10, 12 September 2012


Full id: C2442_Adipocyte_Cardiac_Mesenchymal_heart_mature_Hair_Smooth



Phase1 CAGE Peaks

Hg19::chr17:77020224..77020262,+p1@C1QTNF1
Hg19::chr17:77020273..77020288,+p4@C1QTNF1
Hg19::chr17:77020303..77020314,+p5@C1QTNF1
Hg19::chr17:77020325..77020348,+p2@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
multi-tissue structure1.95e-23347
organism subdivision7.19e-22365
multi-cellular organism5.56e-20659
somite7.06e-2083
paraxial mesoderm7.06e-2083
presomitic mesoderm7.06e-2083
presumptive segmental plate7.06e-2083
trunk paraxial mesoderm7.06e-2083
presumptive paraxial mesoderm7.06e-2083
anatomical cluster1.04e-19286
multilaminar epithelium1.63e-1982
cell layer4.53e-19312
epithelium5.54e-19309
trunk mesenchyme6.99e-18143
dermomyotome7.33e-1870
splanchnic layer of lateral plate mesoderm2.01e-1784
anatomical conduit4.01e-17241
muscle tissue4.67e-1763
musculature4.67e-1763
musculature of body4.67e-1763
skeletal muscle tissue1.13e-1661
striated muscle tissue1.13e-1661
myotome1.13e-1661
anatomical system3.03e-16625
trunk4.50e-16216
anatomical group6.25e-16626
primary circulatory organ1.59e-1527
embryonic structure5.31e-15605
developing anatomical structure5.31e-15605
germ layer8.52e-15604
embryonic tissue8.52e-15604
presumptive structure8.52e-15604
epiblast (generic)8.52e-15604
mesenchyme8.69e-15238
entire embryonic mesenchyme8.69e-15238
embryo1.04e-14612
heart1.19e-1324
primitive heart tube1.19e-1324
primary heart field1.19e-1324
anterior lateral plate mesoderm1.19e-1324
heart tube1.19e-1324
heart primordium1.19e-1324
cardiac mesoderm1.19e-1324
cardiogenic plate1.19e-1324
heart rudiment1.19e-1324
epithelial tube2.70e-13118
adult organism1.42e-12115
circulatory system4.69e-12113
tube1.63e-11194
systemic artery2.29e-1133
systemic arterial system2.29e-1133
vasculature2.66e-1179
vascular system2.66e-1179
artery2.74e-1142
arterial blood vessel2.74e-1142
arterial system2.74e-1142
cardiovascular system8.20e-11110
blood vessel1.17e-1060
epithelial tube open at both ends1.17e-1060
blood vasculature1.17e-1060
vascular cord1.17e-1060
unilaminar epithelium1.71e-10138
vessel2.32e-1069
compound organ3.51e-1069
organ3.03e-08511
primordium3.58e-08168
surface structure4.68e-0895
mesoderm2.37e-07448
mesoderm-derived structure2.37e-07448
presumptive mesoderm2.37e-07448
smooth muscle tissue7.42e-0715
Disease
Ontology termp-valuen
ovarian cancer5.50e-0714


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#1012748.221841637010680.0002187871180958320.00248747091517642



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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