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Coexpression cluster:C2079

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Full id: C2079_epididymis_kidney_liver_papillotubular_Hepatocyte_colon_hepatoblastoma



Phase1 CAGE Peaks

  Short description
Hg19::chr10:91316455..91316462,- p4@SLC16A12
Hg19::chr3:114464766..114464816,- p@chr3:114464766..114464816
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Hg19::chr3:114464819..114464840,- p@chr3:114464819..114464840
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Hg19::chr3:114464843..114464849,- p@chr3:114464843..114464849
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Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
metabolising cell6.10e-1012
endopolyploid cell6.10e-1012
parenchymal cell6.10e-1012
polyploid cell6.10e-1012
hepatocyte6.10e-1012
kidney cell1.99e-0917
kidney epithelial cell1.99e-0917
epithelial cell of nephron8.77e-0715
Uber Anatomy
Ontology termp-valuen
abdomen element2.93e-1654
abdominal segment element2.93e-1654
trunk region element1.30e-15101
abdominal segment of trunk4.51e-1560
abdomen4.51e-1560
subdivision of trunk9.72e-13112
digestive tract diverticulum3.40e-1223
cavitated compound organ3.46e-1231
sac4.01e-1226
subdivision of digestive tract6.90e-12118
kidney1.17e-1126
kidney mesenchyme1.17e-1126
upper urinary tract1.17e-1126
kidney rudiment1.17e-1126
kidney field1.17e-1126
adult organism1.28e-11114
hepatic diverticulum5.51e-1122
liver primordium5.51e-1122
epithelial sac5.83e-1125
urinary system structure5.85e-1147
epithelium of foregut-midgut junction8.37e-1125
anatomical boundary8.37e-1125
hepatobiliary system8.37e-1125
foregut-midgut junction8.37e-1125
septum transversum8.37e-1125
trunk8.41e-11199
renal system1.29e-1048
digestive system1.73e-10145
digestive tract1.73e-10145
primitive gut1.73e-10145
gut epithelium3.49e-1054
anatomical cluster4.22e-10373
immaterial anatomical entity4.51e-10117
mesenchyme7.17e-10160
entire embryonic mesenchyme7.17e-10160
multi-tissue structure1.86e-09342
compound organ2.51e-0968
endoderm-derived structure3.76e-09160
endoderm3.76e-09160
presumptive endoderm3.76e-09160
liver4.56e-0919
digestive gland4.56e-0919
liver bud4.56e-0919
organism subdivision1.04e-08264
endo-epithelium1.40e-0882
excretory tube3.90e-0816
kidney epithelium3.90e-0816
organ1.54e-07503
intestine3.89e-0717
male genital duct4.07e-073
internal male genitalia4.07e-073
epithelial tube4.98e-07117
anatomical conduit6.04e-07240
nephron epithelium8.77e-0715
renal tubule8.77e-0715
nephron tubule8.77e-0715
nephron8.77e-0715
uriniferous tubule8.77e-0715
nephrogenic mesenchyme8.77e-0715


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CEBPB#105135.978360719368610.007153832484726970.0297144094365415
FOSL2#2355312.69765045342130.000787568572975710.00616542044771832
NR3C1#2908414.9730233311731.98868032687801e-050.000441811922269331
USF1#739134.771124457905970.01370465887188020.048266704927507



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.