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Coexpression cluster:C1901: Difference between revisions

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|tf_chipseq_enrich=EGR1#1958;5:4.98817909481014:0.000323739800059071:0.00330961834165714!EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00110911302918578!RAD21#5885;5:10.3550338954563:8.39503550283973e-06:0.00022958080986674!USF1#7391;5:6.36149927720796:9.59569864925045e-05:0.00136963943040736!YY1#7528;5:4.91117074985386:0.0003499314082136:0.0035283342674667
|tf_chipseq_enrich=EGR1#1958;5:4.98817909481014:0.000323739800059071:0.00330961834165714!EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00110911302918578!RAD21#5885;5:10.3550338954563:8.39503550283973e-06:0.00022958080986674!USF1#7391;5:6.36149927720796:9.59569864925045e-05:0.00136963943040736!YY1#7528;5:4.91117074985386:0.0003499314082136:0.0035283342674667
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}}
}}

Revision as of 15:10, 26 November 2012


Full id: C1901_Cardiac_tridermal_Mesenchymal_sacrococcigeal_Hepatic_Smooth_Myoblast



Phase1 CAGE Peaks

Hg19::chr2:27301468..27301496,+p1@EMILIN1
Hg19::chr2:27301500..27301546,+p2@EMILIN1
Hg19::chr2:27301559..27301574,+p3@EMILIN1
Hg19::chr2:27301661..27301672,+p4@EMILIN1
Hg19::chr2:27301682..27301693,+p5@EMILIN1


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
dense mesenchyme tissue3.87e-2773
somite9.99e-2771
presomitic mesoderm9.99e-2771
presumptive segmental plate9.99e-2771
dermomyotome9.99e-2771
trunk paraxial mesoderm9.99e-2771
paraxial mesoderm1.80e-2672
presumptive paraxial mesoderm1.80e-2672
muscle tissue2.70e-2564
musculature2.70e-2564
musculature of body2.70e-2564
epithelial vesicle8.68e-2578
skeletal muscle tissue1.49e-2462
striated muscle tissue1.49e-2462
myotome1.49e-2462
trunk mesenchyme7.10e-20122
multilaminar epithelium2.22e-1983
mesenchyme1.27e-18160
entire embryonic mesenchyme1.27e-18160
splanchnic layer of lateral plate mesoderm2.48e-1483
multi-cellular organism1.88e-13656
mesoderm9.09e-13315
mesoderm-derived structure9.09e-13315
presumptive mesoderm9.09e-13315
tissue9.45e-13773
unilaminar epithelium1.72e-12148
multi-tissue structure2.70e-12342
vasculature6.51e-1278
vascular system6.51e-1278
circulatory system1.13e-11112
cardiovascular system1.99e-11109
anatomical system9.47e-10624
epithelial tube9.95e-10117
anatomical group1.45e-09625
cell layer2.11e-09309
epithelial tube open at both ends2.34e-0959
blood vessel2.34e-0959
blood vasculature2.34e-0959
vascular cord2.34e-0959
heart3.62e-0924
primitive heart tube3.62e-0924
primary heart field3.62e-0924
anterior lateral plate mesoderm3.62e-0924
heart tube3.62e-0924
heart primordium3.62e-0924
cardiac mesoderm3.62e-0924
cardiogenic plate3.62e-0924
heart rudiment3.62e-0924
primary circulatory organ3.88e-0927
epithelium4.19e-09306
systemic artery5.76e-0933
systemic arterial system5.76e-0933
vessel5.97e-0968
artery8.96e-0942
arterial blood vessel8.96e-0942
arterial system8.96e-0942
smooth muscle tissue1.39e-0815
germ layer2.15e-08560
germ layer / neural crest2.15e-08560
embryonic tissue2.15e-08560
presumptive structure2.15e-08560
germ layer / neural crest derived structure2.15e-08560
epiblast (generic)2.15e-08560
organism subdivision2.19e-08264
embryonic structure3.69e-08564
trunk8.66e-08199
musculoskeletal system1.27e-07167
anatomical cluster1.32e-07373


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
EGR1#195854.988179094810140.0003237398000590710.00330961834165714
EP300#203356.77394172622327.00901578206049e-050.00110911302918578
RAD21#5885510.35503389545638.39503550283973e-060.00022958080986674
USF1#739156.361499277207969.59569864925045e-050.00136963943040736
YY1#752854.911170749853860.00034993140821360.0035283342674667



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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