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Coexpression cluster:C4281

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Full id: C4281_renal_hepatocellular_Hepatocyte_liver_mesothelioma_mucinous_signet



Phase1 CAGE Peaks

  Short description
Hg19::chr3:129375541..129375549,- p23@TMCC1
Hg19::chr3:129375590..129375615,- p7@TMCC1
Hg19::chrX:74869077..74869082,- p@chrX:74869077..74869082
-


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
metabolising cell1.32e-1812
endopolyploid cell1.32e-1812
parenchymal cell1.32e-1812
polyploid cell1.32e-1812
hepatocyte1.32e-1812
mucus secreting cell2.37e-101
Uber Anatomy
Ontology termp-valuen
hepatic diverticulum8.40e-2522
liver primordium8.40e-2522
digestive tract diverticulum1.11e-2323
liver2.52e-2219
digestive gland2.52e-2219
liver bud2.52e-2219
epithelial sac1.04e-2125
epithelium of foregut-midgut junction1.04e-2125
anatomical boundary1.04e-2125
hepatobiliary system1.04e-2125
foregut-midgut junction1.04e-2125
septum transversum1.04e-2125
sac7.75e-2126
exocrine gland2.11e-1331
exocrine system2.11e-1331
abdomen element4.41e-1254
abdominal segment element4.41e-1254
endocrine gland8.79e-1235
endocrine system1.39e-1145
abdominal segment of trunk9.64e-1160
abdomen9.64e-1160
gut epithelium1.68e-0954
trunk region element8.19e-09101
subdivision of trunk8.40e-08112
endo-epithelium1.84e-0782
foregut5.86e-0787
Disease
Ontology termp-valuen
mucinous adenocarcinoma2.37e-101
carcinoma9.55e-07106


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
FOSL2#2355211.28680040304110.0100534586973120.0376874792853038
HNF4A#3172215.42152690863580.005444210486686610.0246847225414197
HNF4G#3174219.16894835096450.003543986611284220.0179788418757426
RXRA#6256213.38307809275550.007196434429465730.029834408358962
SP1#666735.69838137814090.005403962701712170.0247222594333574



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.