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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4540_serous_renal_Hepatocyte_signet_gall_liver_kidney
|full_id=C4540_serous_renal_Hepatocyte_signet_gall_liver_kidney
|id=C4540
|id=C4540

Revision as of 17:38, 12 September 2012


Full id: C4540_serous_renal_Hepatocyte_signet_gall_liver_kidney



Phase1 CAGE Peaks

Hg19::chr6:107235234..107235237,-p3@LOC100422737
Hg19::chr6:107235249..107235267,-p1@LOC100422737
Hg19::chr6:107235287..107235303,-p2@LOC100422737


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 cell6.97e-1612
endopolyploid cell6.97e-1612
parenchymal cell6.97e-1612
polyploid cell6.97e-1612
hepatocyte6.97e-1612
kidney cell2.22e-0718
kidney epithelial cell2.22e-0718
endodermal cell3.82e-0759
Uber Anatomy
Ontology termp-valuen
abdomen element2.29e-2455
abdominal segment element2.29e-2455
abdominal segment of trunk1.78e-2161
abdomen1.78e-2161
epithelium of foregut-midgut junction1.33e-1725
anatomical boundary1.33e-1725
hepatobiliary system1.33e-1725
foregut-midgut junction1.33e-1725
septum transversum1.33e-1725
hepatic diverticulum1.18e-1622
liver primordium1.18e-1622
liver5.90e-1619
digestive gland5.90e-1619
liver bud5.90e-1619
digestive tract diverticulum7.71e-1623
trunk region element1.49e-15107
epithelial sac2.08e-1425
sac8.94e-1426
immune organ1.21e-1326
gut epithelium2.56e-1154
immaterial anatomical entity6.25e-11126
subdivision of trunk1.52e-10113
cavitated compound organ2.02e-1032
kidney2.21e-1027
kidney mesenchyme2.21e-1027
kidney rudiment2.21e-1027
kidney field2.21e-1027
urinary system structure3.53e-1044
renal system6.75e-1045
exocrine gland4.07e-0931
exocrine system4.07e-0931
endocrine system1.14e-0845
endocrine gland6.93e-0835
endo-epithelium1.61e-0782
mixed endoderm/mesoderm-derived structure2.44e-07130
subdivision of digestive tract2.78e-07129
endodermal part of digestive tract2.78e-07129
gland3.48e-0759
trunk6.82e-07216
Disease
Ontology termp-valuen
adenocarcinoma6.84e-0925
clear cell adenocarcinoma8.35e-092
carcinoma7.78e-07106


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
CEBPB#105137.971147625824820.001974187055288560.01156766841715
EP300#203336.77394172622320.003216880500103790.0168236245643635
FOXA1#3169311.08141974938550.000734755275698670.00583552138697288



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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