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Coexpression cluster:C2836: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2836_Fibroblast_Endothelial_mature_Cardiac_Smooth_mesenchymal_Adipocyte
|full_id=C2836_Fibroblast_Endothelial_mature_Cardiac_Smooth_mesenchymal_Adipocyte
|id=C2836
|id=C2836

Revision as of 15:37, 12 September 2012


Full id: C2836_Fibroblast_Endothelial_mature_Cardiac_Smooth_mesenchymal_Adipocyte



Phase1 CAGE Peaks

Hg19::chr6:112575490..112575527,-p3@LAMA4
Hg19::chr6:112575733..112575755,-p2@LAMA4
Hg19::chr6:112575758..112575776,-p1@LAMA4
Hg19::chr6:112575838..112575847,-p6@LAMA4


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
vasculature5.60e-2679
vascular system5.60e-2679
vessel9.42e-2369
splanchnic layer of lateral plate mesoderm7.01e-2284
blood vessel2.11e-2060
epithelial tube open at both ends2.11e-2060
blood vasculature2.11e-2060
vascular cord2.11e-2060
circulatory system1.51e-19113
cardiovascular system1.97e-19110
organism subdivision2.97e-17365
somite3.39e-1783
paraxial mesoderm3.39e-1783
presomitic mesoderm3.39e-1783
presumptive segmental plate3.39e-1783
trunk paraxial mesoderm3.39e-1783
presumptive paraxial mesoderm3.39e-1783
dermomyotome3.81e-1770
anatomical cluster6.36e-17286
anatomical conduit2.00e-16241
cell layer2.11e-16312
epithelial tube3.81e-16118
muscle tissue5.18e-1663
musculature5.18e-1663
musculature of body5.18e-1663
epithelium1.07e-15309
artery1.40e-1542
arterial blood vessel1.40e-1542
arterial system1.40e-1542
skeletal muscle tissue1.52e-1561
striated muscle tissue1.52e-1561
myotome1.52e-1561
unilaminar epithelium7.93e-15138
systemic artery3.73e-1433
systemic arterial system3.73e-1433
multilaminar epithelium5.06e-1482
trunk mesenchyme5.06e-13143
multi-cellular organism6.78e-13659
tube8.46e-13194
multi-tissue structure6.27e-12347
trunk3.92e-11216
anatomical system5.51e-11625
anatomical group9.35e-11626
endothelium3.57e-1018
blood vessel endothelium3.57e-1018
cardiovascular system endothelium3.57e-1018
aorta1.92e-0921
aortic system1.92e-0921
squamous epithelium9.44e-0925
simple squamous epithelium1.93e-0822
surface structure1.04e-0795
integument1.21e-0745
integumental system1.21e-0745
mesenchyme1.60e-07238
entire embryonic mesenchyme1.60e-07238
heart3.25e-0724
primitive heart tube3.25e-0724
primary heart field3.25e-0724
anterior lateral plate mesoderm3.25e-0724
heart tube3.25e-0724
heart primordium3.25e-0724
cardiac mesoderm3.25e-0724
cardiogenic plate3.25e-0724
heart rudiment3.25e-0724
primary circulatory organ3.61e-0727


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
CTBP2#1488462.71700033932816.45042639894877e-083.96746809587639e-06
GATA2#262439.55869880016550.001818151618357440.0109067166496056
ZNF263#1012736.166381227758010.006539814347975980.0279911344079449



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2836&oldid=2137558"