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Coexpression cluster:C3470: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115063408598293!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167198060391331!JUN#3725;3:12.5128291923363:0.000510331399272625:0.004435996754776!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156449410109305!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00641985145045477
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115063408598293!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167198060391331!JUN#3725;3:12.5128291923363:0.000510331399272625:0.004435996754776!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156449410109305!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00641985145045477
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}}
}}

Revision as of 16:09, 26 November 2012


Full id: C3470_Smooth_Mesothelial_mesothelioma_Synoviocyte_Prostate_normal_mesenchymal



Phase1 CAGE Peaks

Hg19::chr14:96722152..96722166,+p4@BDKRB1
Hg19::chr14:96722171..96722185,+p3@BDKRB1
Hg19::chr14:96722201..96722212,+p5@BDKRB1


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>


Cell Type
Ontology termp-valuen
smooth muscle cell1.15e-1843
smooth muscle myoblast1.15e-1843
muscle precursor cell1.11e-1758
myoblast1.11e-1758
multi-potent skeletal muscle stem cell1.11e-1758
muscle cell6.63e-1655
contractile cell2.28e-1459
electrically responsive cell1.12e-1361
electrically active cell1.12e-1361
non-terminally differentiated cell3.15e-13106
vascular associated smooth muscle cell3.20e-1332
mesodermal cell5.83e-13121
multi fate stem cell7.54e-12427
somatic stem cell2.04e-11433
stem cell7.32e-11441
fibroblast1.10e-1076
aortic smooth muscle cell5.33e-1010
cardiac mesenchymal cell1.39e-084
migratory trunk neural crest cell1.39e-084
skin fibroblast1.99e-0823
mesothelial cell1.03e-0719
enteric smooth muscle cell1.61e-073
smooth muscle cell of large intestine1.61e-073
smooth muscle cell of colon1.61e-073
stromal cell2.54e-0728
preadipocyte3.01e-0712
visceral preadipocyte5.77e-073
Uber Anatomy
Ontology termp-valuen
skeletal muscle tissue4.64e-1662
striated muscle tissue4.64e-1662
myotome4.64e-1662
muscle tissue2.50e-1564
musculature2.50e-1564
musculature of body2.50e-1564
somite4.17e-1371
presomitic mesoderm4.17e-1371
presumptive segmental plate4.17e-1371
dermomyotome4.17e-1371
trunk paraxial mesoderm4.17e-1371
smooth muscle tissue5.76e-1315
paraxial mesoderm7.96e-1372
presumptive paraxial mesoderm7.96e-1372
dense mesenchyme tissue1.49e-1273
multilaminar epithelium2.44e-1183
epithelial vesicle2.66e-1178
systemic artery2.81e-1133
systemic arterial system2.81e-1133
trunk mesenchyme9.24e-11122
blood vessel smooth muscle5.33e-1010
arterial system smooth muscle5.33e-1010
artery smooth muscle tissue5.33e-1010
aorta smooth muscle tissue5.33e-1010
artery3.15e-0942
arterial blood vessel3.15e-0942
arterial system3.15e-0942
unilaminar epithelium1.70e-07148
mesenchyme1.72e-07160
entire embryonic mesenchyme1.72e-07160
epithelial tube open at both ends4.68e-0759
blood vessel4.68e-0759
blood vasculature4.68e-0759
vascular cord4.68e-0759


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
CEBPB#105137.971147625824820.001974187055288560.0115063408598293
EP300#203336.77394172622320.003216880500103790.0167198060391331
JUN#3725312.51282919233630.0005103313992726250.004435996754776
JUND#372736.994663941871030.002921845042734990.0156449410109305
STAT3#6774310.51946499715420.0008589184530415310.00641985145045477



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.