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Coexpression cluster:C4875: Difference between revisions

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|tf_chipseq_enrich=YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331659451675236
|tf_chipseq_enrich=YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331659451675236
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}}
}}

Revision as of 17:01, 26 November 2012


Full id: C4875_leiomyoma_Olfactory_Hair_smallcell_medial_tenocyte_Preadipocyte



Phase1 CAGE Peaks

Hg19::chrX:51638461..51638473,+p7@MAGED1
Hg19::chrX:51638504..51638519,+p5@MAGED1
Hg19::chrX:51638616..51638639,+p4@MAGED1


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
epithelial vesicle2.22e-1478
dense mesenchyme tissue6.41e-1473
paraxial mesoderm1.89e-1372
presumptive paraxial mesoderm1.89e-1372
somite2.63e-1371
presomitic mesoderm2.63e-1371
presumptive segmental plate2.63e-1371
dermomyotome2.63e-1371
trunk paraxial mesoderm2.63e-1371
trunk mesenchyme3.72e-13122
mesenchyme6.68e-13160
entire embryonic mesenchyme6.68e-13160
skeletal muscle tissue9.67e-1262
striated muscle tissue9.67e-1262
myotome9.67e-1262
multilaminar epithelium1.00e-1183
cell layer1.74e-11309
epithelium2.38e-11306
muscle tissue4.22e-1164
musculature4.22e-1164
musculature of body4.22e-1164
unilaminar epithelium6.95e-11148
vasculature2.90e-0978
vascular system2.90e-0978
multi-tissue structure7.40e-09342
artery1.20e-0842
arterial blood vessel1.20e-0842
arterial system1.20e-0842
splanchnic layer of lateral plate mesoderm1.53e-0883
multi-cellular organism1.63e-08656
epithelial tube8.11e-08117
anatomical cluster1.05e-07373
trunk1.25e-07199
epithelial tube open at both ends2.03e-0759
blood vessel2.03e-0759
blood vasculature2.03e-0759
vascular cord2.03e-0759
organism subdivision2.27e-07264
systemic artery2.62e-0733
systemic arterial system2.62e-0733
vessel4.46e-0768


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
YY1#752834.911170749853860.008441455341808260.0331659451675236



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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