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Coexpression cluster:C4458

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Full id: C4458_small_renal_kidney_Hepatocyte_clear_colon_argyrophil



Phase1 CAGE Peaks

  Short description
Hg19::chr5:125706998..125707018,+ p4@GRAMD3
Hg19::chr5:125707019..125707032,+ p16@GRAMD3
Hg19::chr6:116381918..116381977,- p1@FRK


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
disease_data


Cell Type
Ontology termp-valuen
epithelial cell5.83e-25254
endodermal cell3.58e-2059
endo-epithelial cell4.13e-1443
kidney cell3.53e-0718
kidney epithelial cell3.53e-0718
epithelial cell of alimentary canal6.38e-0721
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure9.27e-30169
endoderm9.27e-30169
presumptive endoderm9.27e-30169
subdivision of digestive tract2.45e-28129
endodermal part of digestive tract2.45e-28129
digestive system1.71e-27155
digestive tract1.71e-27155
primitive gut1.71e-27155
mixed endoderm/mesoderm-derived structure2.63e-23130
foregut9.47e-1898
mesenchyme2.43e-17238
entire embryonic mesenchyme2.43e-17238
immaterial anatomical entity4.18e-17126
endo-epithelium6.30e-1682
trunk region element6.89e-16107
renal system3.32e-1545
multi-tissue structure8.03e-15347
urinary system structure1.23e-1444
respiratory system8.79e-1472
subdivision of trunk1.46e-13113
abdomen element2.59e-1355
abdominal segment element2.59e-1355
abdominal segment of trunk5.10e-1361
abdomen5.10e-1361
organ3.28e-12511
anatomical space1.14e-11104
gut epithelium3.52e-1154
intermediate mesoderm9.40e-1137
respiratory tract1.31e-1053
orifice3.47e-1035
trunk4.56e-10216
compound organ5.57e-1069
duct8.52e-1026
primordium1.56e-09168
hindgut1.65e-0919
respiratory primordium4.91e-0938
endoderm of foregut4.91e-0938
anatomical cavity6.71e-0970
cavitated compound organ6.98e-0932
sac8.42e-0926
epithelium of foregut-midgut junction9.71e-0925
anatomical boundary9.71e-0925
hepatobiliary system9.71e-0925
foregut-midgut junction9.71e-0925
septum transversum9.71e-0925
gland3.15e-0859
epithelial sac3.27e-0825
gastrointestinal system4.73e-0835
kidney5.71e-0827
kidney mesenchyme5.71e-0827
kidney rudiment5.71e-0827
kidney field5.71e-0827
intraembryonic coelom5.89e-0821
digestive tract diverticulum1.58e-0723
anatomical cluster1.64e-07286
anatomical conduit1.72e-07241
segment of respiratory tract1.84e-0746
epithelial bud2.35e-0737
body cavity precursor2.95e-0763
exocrine gland4.10e-0731
exocrine system4.10e-0731
mesonephros4.64e-0718
pronephros4.64e-0718
nephrogenic cord4.64e-0718
pronephric mesoderm4.64e-0718
rostral part of nephrogenic cord4.64e-0718
presumptive pronephric mesoderm4.64e-0718
hepatic diverticulum5.95e-0722
liver primordium5.95e-0722
organ part6.19e-07219
reproductive structure6.43e-0759
reproductive system6.43e-0759
larynx7.49e-079
urogenital ridge7.94e-0720
Disease
Ontology termp-valuen
carcinoma5.87e-27106
cell type cancer1.75e-20143
adenocarcinoma2.07e-1225
cancer2.73e-09235
disease of cellular proliferation5.33e-09239


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
CTCF#1066435.360256373075030.0064925092527670.0280821326037329



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.