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Coexpression cluster:C2844: Difference between revisions

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|tf_chipseq_enrich=RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172778355882891!SMARCC2#6601;2:47.0776872134488:0.000666928296709587:0.00545103493348353
|tf_chipseq_enrich=RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172778355882891!SMARCC2#6601;2:47.0776872134488:0.000666928296709587:0.00545103493348353
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}}
}}

Revision as of 15:45, 26 November 2012


Full id: C2844_Smooth_mesenchymal_Fibroblast_Preadipocyte_H9_Mesenchymal_Small



Phase1 CAGE Peaks

Hg19::chr6:136336050..136336056,-p@chr6:136336050..136336056
-
Hg19::chr6:83073422..83073436,+p10@TPBG
Hg19::chr6:83073900..83073915,+p16@TPBG
Hg19::chr9:133736506..133736518,+p@chr9:133736506..133736518
+


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
multilaminar epithelium7.48e-1283
dense mesenchyme tissue2.31e-1173
somite4.77e-1171
presomitic mesoderm4.77e-1171
presumptive segmental plate4.77e-1171
dermomyotome4.77e-1171
trunk paraxial mesoderm4.77e-1171
paraxial mesoderm1.00e-1072
presumptive paraxial mesoderm1.00e-1072
skeletal muscle tissue1.85e-0962
striated muscle tissue1.85e-0962
myotome1.85e-0962
epithelial vesicle5.35e-0978
muscle tissue7.59e-0964
musculature7.59e-0964
musculature of body7.59e-0964
artery6.21e-0842
arterial blood vessel6.21e-0842
arterial system6.21e-0842
systemic artery8.41e-0833
systemic arterial system8.41e-0833
trunk mesenchyme3.53e-07122
right ovary7.46e-075
Disease
Ontology termp-valuen
ovarian cancer4.00e-1114


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#588537.766275421592250.0033411193858720.0172778355882891
SMARCC2#6601247.07768721344880.0006669282967095870.00545103493348353



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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