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Revision as of 05:46, 21 May 2012

Full id: C4281_renal_hepatocellular_Hepatocyte_liver_mesothelioma_mucinous_signet

Phase1 CAGE Peaks

  Short description
Hg19::chr3:129375541..129375549,- p23@TMCC1
Hg19::chr3:129375590..129375615,- p7@TMCC1
Hg19::chrX:74869077..74869082,- p@chrX:74869077..74869082

Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset

No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset

No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset


Uber Anatomy
Ontology termp-valuen
abdomen element4.89e-1255
abdominal segment element4.89e-1255
epithelium of foregut-midgut junction1.58e-1125
anatomical boundary1.58e-1125
hepatobiliary system1.58e-1125
foregut-midgut junction1.58e-1125
septum transversum1.58e-1125
hepatic diverticulum1.83e-1122
liver primordium1.83e-1122
digestive gland2.15e-1119
liver bud2.15e-1119
digestive tract diverticulum7.62e-1123
abdominal segment of trunk2.54e-1061
epithelial sac9.31e-1025
immune organ4.18e-0926
anatomical conduit7.81e-08241
gut epithelium3.28e-0754
epithelial tube5.27e-07118
trunk region element5.96e-07107

Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs

Jaspar motifs

Novel motifs

JASPAR motifs



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset


No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.

link to data source

This analysis result is provided for C0 - C305 clusters.