Personal tools

Coexpression cluster:C768


Revision as of 07:41, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search

Full id: C768_Hepatocyte_liver_cervical_Hep2_epitheloid_large_nonsmall

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

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>

Cell Type
Ontology termp-valuen
metabolising cell9.59e-1212
endopolyploid cell9.59e-1212
parenchymal cell9.59e-1212
polyploid cell9.59e-1212
epithelial cell4.22e-09253
Uber Anatomy
Ontology termp-valuen
upper respiratory tract2.87e-2419
subdivision of digestive tract4.57e-19118
respiratory primordium6.20e-1738
endoderm of foregut6.20e-1738
digestive system2.92e-16145
digestive tract2.92e-16145
primitive gut2.92e-16145
endoderm-derived structure2.71e-14160
presumptive endoderm2.71e-14160
digestive gland4.20e-1419
liver bud4.20e-1419
epithelium of foregut-midgut junction1.34e-1325
anatomical boundary1.34e-1325
hepatobiliary system1.34e-1325
foregut-midgut junction1.34e-1325
septum transversum1.34e-1325
segment of respiratory tract2.77e-1347
hepatic diverticulum4.64e-1222
liver primordium4.64e-1222
digestive tract diverticulum1.69e-1123
respiratory tract2.75e-1154
small intestine8.93e-114
epithelial sac1.66e-1025
organ system subdivision9.65e-09223
exocrine gland2.66e-0831
exocrine system2.66e-0831
respiratory system1.12e-0774
endocrine gland2.98e-0735
Ontology termp-valuen
cell type cancer2.44e-13143
disease of cellular proliferation5.71e-07239

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.