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Coexpression cluster:C4524: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4524_Fibroblast_Smooth_Preadipocyte_Lens_CD14_mesenchymal_serous
|full_id=C4524_Fibroblast_Smooth_Preadipocyte_Lens_CD14_mesenchymal_serous
|id=C4524
|id=C4524

Revision as of 17:37, 12 September 2012


Full id: C4524_Fibroblast_Smooth_Preadipocyte_Lens_CD14_mesenchymal_serous



Phase1 CAGE Peaks

Hg19::chr5:82767383..82767423,+p3@VCAN
Hg19::chr5:82767487..82767510,+p5@VCAN
Hg19::chr5:82767523..82767543,+p4@VCAN


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
multi-cellular organism4.15e-19659
anatomical system3.77e-15625
anatomical group6.09e-15626
musculoskeletal system6.38e-14167
embryo8.81e-14612
somite2.99e-1283
paraxial mesoderm2.99e-1283
presomitic mesoderm2.99e-1283
presumptive segmental plate2.99e-1283
trunk paraxial mesoderm2.99e-1283
presumptive paraxial mesoderm2.99e-1283
skeletal muscle tissue5.83e-1261
striated muscle tissue5.83e-1261
myotome5.83e-1261
embryonic structure7.03e-12605
developing anatomical structure7.03e-12605
muscle tissue1.46e-1163
musculature1.46e-1163
musculature of body1.46e-1163
dermomyotome1.50e-1170
germ layer1.51e-11604
embryonic tissue1.51e-11604
presumptive structure1.51e-11604
epiblast (generic)1.51e-11604
tissue1.88e-09787
organ1.38e-08511
multilaminar epithelium5.55e-0882
heart6.07e-0824
primitive heart tube6.07e-0824
primary heart field6.07e-0824
anterior lateral plate mesoderm6.07e-0824
heart tube6.07e-0824
heart primordium6.07e-0824
cardiac mesoderm6.07e-0824
cardiogenic plate6.07e-0824
heart rudiment6.07e-0824
organism subdivision9.02e-08365
mesoderm1.07e-07448
mesoderm-derived structure1.07e-07448
presumptive mesoderm1.07e-07448
lateral plate mesoderm1.47e-07216
trunk mesenchyme1.82e-07143
primary circulatory organ2.67e-0727
Disease
Ontology termp-valuen
ovarian cancer4.60e-0814


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
RAD21#5885310.35503389545630.0009004912073565420.0066770607884352
ZNF263#1012738.221841637010680.001799043925565870.0109960992884751



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:C4524&oldid=2139434"