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Coexpression cluster:C2059: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00815280776754614!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00433348824966487!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172598885858973!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195677598024727!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248018102972002
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00815280776754614!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00433348824966487!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172598885858973!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195677598024727!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248018102972002
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}}
}}

Revision as of 15:16, 26 November 2012


Full id: C2059_Myoblast_prostate_tridermal_mucinous_myxofibrosarcoma_mesenchymal_osteosarcoma



Phase1 CAGE Peaks

Hg19::chr10:33623685..33623700,-p7@NRP1
Hg19::chr10:33623764..33623777,-p6@NRP1
Hg19::chr10:33623784..33623806,-p1@NRP1
Hg19::chr10:33623826..33623835,-p9@NRP1


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
mesenchyme2.15e-19160
entire embryonic mesenchyme2.15e-19160
multi-cellular organism1.69e-17656
trunk mesenchyme4.49e-17122
epithelial vesicle6.99e-1778
somite2.83e-1671
presomitic mesoderm2.83e-1671
presumptive segmental plate2.83e-1671
dermomyotome2.83e-1671
trunk paraxial mesoderm2.83e-1671
dense mesenchyme tissue3.04e-1673
organism subdivision5.97e-16264
paraxial mesoderm8.28e-1672
presumptive paraxial mesoderm8.28e-1672
trunk9.55e-16199
unilaminar epithelium3.03e-15148
anatomical system9.16e-15624
multilaminar epithelium9.28e-1583
anatomical group1.93e-14625
skeletal muscle tissue3.35e-1462
striated muscle tissue3.35e-1462
myotome3.35e-1462
epithelial tube8.73e-14117
muscle tissue9.30e-1464
musculature9.30e-1464
musculature of body9.30e-1464
vasculature2.00e-1378
vascular system2.00e-1378
splanchnic layer of lateral plate mesoderm3.56e-1283
cell layer3.32e-11309
vessel7.00e-1168
epithelium8.00e-11306
multi-tissue structure2.02e-10342
anatomical cluster3.11e-10373
epithelial tube open at both ends3.94e-1059
blood vessel3.94e-1059
blood vasculature3.94e-1059
vascular cord3.94e-1059
circulatory system7.21e-10112
artery7.87e-1042
arterial blood vessel7.87e-1042
arterial system7.87e-1042
cardiovascular system1.57e-09109
systemic artery2.19e-0933
systemic arterial system2.19e-0933
surface structure2.22e-0999
integument1.26e-0846
integumental system1.26e-0846
skin of body2.45e-0841
embryo3.51e-08592
developing anatomical structure4.23e-08581
mesoderm8.78e-08315
mesoderm-derived structure8.78e-08315
presumptive mesoderm8.78e-08315
aorta2.53e-0721
aortic system2.53e-0721
anatomical conduit3.08e-07240
germ layer3.65e-07560
germ layer / neural crest3.65e-07560
embryonic tissue3.65e-07560
presumptive structure3.65e-07560
germ layer / neural crest derived structure3.65e-07560
epiblast (generic)3.65e-07560
embryonic structure4.59e-07564


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#1066445.360256373075030.001211145381643620.00815280776754614
EP300#203346.77394172622320.0004748459821442640.00433348824966487
RAD21#588537.766275421592250.0033411193858720.0172598885858973
REST#597837.237521537096020.004104697304192610.0195677598024727
ZNF263#1012748.221841637010680.0002187871180958320.00248018102972002



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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