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Coexpression cluster:C3083: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3083_Osteoblast_Synoviocyte_tenocyte_Adipocyte_Preadipocyte_Mesenchymal_Sertoli
|full_id=C3083_Osteoblast_Synoviocyte_tenocyte_Adipocyte_Preadipocyte_Mesenchymal_Sertoli
|id=C3083
|id=C3083

Revision as of 15:56, 12 September 2012


Full id: C3083_Osteoblast_Synoviocyte_tenocyte_Adipocyte_Preadipocyte_Mesenchymal_Sertoli



Phase1 CAGE Peaks

Hg19::chr11:114167069..114167146,+p1@NNMT
Hg19::chr11:114167149..114167162,+p4@NNMT
Hg19::chr11:114167202..114167221,+p3@NNMT


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
trunk mesenchyme8.64e-25143
epithelial tube5.17e-20118
somite1.04e-1983
paraxial mesoderm1.04e-1983
presomitic mesoderm1.04e-1983
presumptive segmental plate1.04e-1983
trunk paraxial mesoderm1.04e-1983
presumptive paraxial mesoderm1.04e-1983
trunk1.35e-19216
dermomyotome4.32e-1970
unilaminar epithelium6.78e-18138
skeletal muscle tissue1.33e-1761
striated muscle tissue1.33e-1761
myotome1.33e-1761
muscle tissue1.70e-1763
musculature1.70e-1763
musculature of body1.70e-1763
mesenchyme2.59e-17238
entire embryonic mesenchyme2.59e-17238
multilaminar epithelium1.02e-1682
organism subdivision1.64e-16365
multi-tissue structure1.66e-15347
vasculature1.72e-1579
vascular system1.72e-1579
splanchnic layer of lateral plate mesoderm2.45e-1584
epithelium3.49e-15309
cell layer5.45e-15312
anatomical cluster1.48e-14286
vessel9.89e-1369
circulatory system9.05e-12113
cardiovascular system9.16e-12110
blood vessel1.88e-1160
epithelial tube open at both ends1.88e-1160
blood vasculature1.88e-1160
vascular cord1.88e-1160
anatomical conduit1.73e-10241
multi-cellular organism1.76e-10659
mesoderm1.56e-09448
mesoderm-derived structure1.56e-09448
presumptive mesoderm1.56e-09448
artery1.88e-0942
arterial blood vessel1.88e-0942
arterial system1.88e-0942
anatomical system1.70e-08625
anatomical group2.74e-08626
tube4.69e-08194
adipose tissue8.20e-0814
heart1.42e-0724
primitive heart tube1.42e-0724
primary heart field1.42e-0724
anterior lateral plate mesoderm1.42e-0724
heart tube1.42e-0724
heart primordium1.42e-0724
cardiac mesoderm1.42e-0724
cardiogenic plate1.42e-0724
heart rudiment1.42e-0724
systemic artery1.63e-0733
systemic arterial system1.63e-0733
primary circulatory organ2.84e-0727
surface structure3.23e-0795
integument6.70e-0745
integumental system6.70e-0745


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#105137.971147625824820.001974187055288560.0114928718989566
CTCF#1066435.360256373075030.0064925092527670.027825153836831
EP300#203336.77394172622320.003216880500103790.0166849315926867
NR3C1#2908314.9730233311730.0002978331194675480.00307852268052962
STAT1#6772320.70658749719920.0001125992441046670.00154408514378247
STAT3#6774310.51946499715420.0008589184530415310.00641480151009757
USF1#739136.361499277207960.00388404057290560.0189509606817887



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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