Personal tools

Coexpression cluster:C1345


Revision as of 05:50, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search

Full id: C1345_Intestinal_Hepatocyte_small_testis_colon_Prostate_temporal

Phase1 CAGE Peaks


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

6.15571812123322e-050.03896569570740632130Biological oxidations (Reactome):REACT_13433

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

GO IDGO nameFDR corrected p-value
GO:0004062aryl sulfotransferase activity0.0286092712752857
GO:0006749glutathione metabolic process0.038596371797347
GO:0006584catecholamine metabolic process0.038596371797347
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.038596371797347
GO:0018958phenol metabolic process0.038596371797347

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>

Cell Type
Ontology termp-valuen
metabolising cell1.34e-2412
endopolyploid cell1.34e-2412
parenchymal cell1.34e-2412
polyploid cell1.34e-2412
endodermal cell6.72e-1158
intestinal epithelial cell3.02e-074
Uber Anatomy
Ontology termp-valuen
gastrointestinal system5.71e-3225
digestive tract diverticulum5.12e-2523
digestive gland6.97e-2519
liver bud6.97e-2519
epithelium of foregut-midgut junction8.58e-2325
anatomical boundary8.58e-2325
hepatobiliary system8.58e-2325
foregut-midgut junction8.58e-2325
septum transversum8.58e-2325
subdivision of digestive tract9.28e-23118
hepatic diverticulum2.72e-2122
liver primordium2.72e-2122
large intestine1.05e-1911
digestive system1.84e-19145
digestive tract1.84e-19145
primitive gut1.84e-19145
gut epithelium1.89e-1954
epithelial sac1.47e-1825
endoderm-derived structure3.40e-17160
presumptive endoderm3.40e-17160
abdomen element2.29e-1654
abdominal segment element2.29e-1654
endocrine gland9.47e-1635
exocrine gland1.11e-1431
exocrine system1.11e-1431
abdominal segment of trunk1.78e-1460
endocrine system2.43e-1445
small intestine3.07e-124
lower digestive tract1.79e-115
organ system subdivision7.82e-11223
trunk region element6.68e-09101
multi-tissue structure1.30e-08342
anatomical cluster2.25e-07373
vermiform appendix2.35e-071
intestinal mucosa3.02e-074
wall of intestine3.02e-074
gastrointestinal system mucosa3.02e-074
gastrointestinal system epithelium3.02e-074
intestinal epithelium3.02e-074

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



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

No analysis results for this cluster

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.