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Coexpression cluster:C2364

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Full id: C2364_small_rectum_colon_hepatocellular_duodenum_temporal_umbilical



Phase1 CAGE Peaks

Hg19::chr16:2034692..2034713,+p7@GFER
Hg19::chr19:1285977..1285989,+p3@EFNA2
Hg19::chr19:18451962..18451992,+p@chr19:18451962..18451992
+
Hg19::chr7:1022811..1022824,+p1@CYP2W1


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


GO IDGO nameFDR corrected p-value
GO:0016972thiol oxidase activity0.00706360170550267
GO:0016670oxidoreductase activity, acting on sulfur group of donors, oxygen as acceptor0.00706360170550267
GO:0046875ephrin receptor binding0.00706360170550267
GO:0016667oxidoreductase activity, acting on sulfur group of donors0.0255882228825599
GO:0016491oxidoreductase activity0.0487832483272223



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 cell8.36e-0912
endopolyploid cell8.36e-0912
parenchymal cell8.36e-0912
polyploid cell8.36e-0912
hepatocyte8.36e-0912
endodermal cell4.94e-0858
Uber Anatomy
Ontology termp-valuen
gastrointestinal system3.03e-2025
intestine1.83e-1917
large intestine2.08e-1311
subdivision of digestive tract1.90e-12118
digestive tract diverticulum2.75e-1123
digestive system1.37e-10145
digestive tract1.37e-10145
primitive gut1.37e-10145
lower digestive tract1.78e-105
epithelium of foregut-midgut junction4.00e-1025
anatomical boundary4.00e-1025
hepatobiliary system4.00e-1025
foregut-midgut junction4.00e-1025
septum transversum4.00e-1025
endoderm-derived structure8.92e-10160
endoderm8.92e-10160
presumptive endoderm8.92e-10160
sac9.76e-1026
hepatic diverticulum1.40e-0922
liver primordium1.40e-0922
liver3.50e-0919
digestive gland3.50e-0919
liver bud3.50e-0919
colon1.11e-089
epithelial sac3.22e-0825
rectum7.53e-084
organ system subdivision3.83e-07223


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
HNF4A#3172317.34921777221530.0003125641557482750.00321456305880788
HNF4G#3174214.37671126322340.006924169980439180.0293011907855384



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.