Personal tools

Coexpression cluster:C1345


Revision as of 04:52, 12 September 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>disease_data<br>

Cell Type
Ontology termp-valuen
metabolising cell3.27e-0712
endopolyploid cell3.27e-0712
parenchymal cell3.27e-0712
polyploid cell3.27e-0712
endodermal cell3.53e-0759
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.78e-19169
presumptive endoderm3.78e-19169
digestive system4.41e-19155
digestive tract4.41e-19155
primitive gut4.41e-19155
subdivision of digestive tract1.58e-17129
endodermal part of digestive tract1.58e-17129
mixed endoderm/mesoderm-derived structure2.14e-14130
epithelium of foregut-midgut junction6.30e-1225
anatomical boundary6.30e-1225
hepatobiliary system6.30e-1225
foregut-midgut junction6.30e-1225
septum transversum6.30e-1225
adult organism1.87e-11115
digestive tract diverticulum1.94e-1023
hepatic diverticulum1.15e-0922
liver primordium1.15e-0922
gut epithelium2.24e-0954
epithelial sac8.18e-0925
abdomen element4.20e-0855
abdominal segment element4.20e-0855
trunk region element4.84e-08107
digestive gland4.94e-0819
liver bud4.94e-0819
immune organ5.30e-0826
immaterial anatomical entity1.51e-07126
gastrointestinal system1.74e-0735
exocrine gland4.84e-0731
exocrine system4.84e-0731
respiratory system6.69e-0772
Ontology termp-valuen
cell type cancer3.12e-08143

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.