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Coexpression cluster:C794

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Full id: C794_small_signet_adenocarcinoma_colon_Hepatocyte_gall_liver



Phase1 CAGE Peaks

Hg19::chr11:123461510..123461537,+p@chr11:123461510..123461537
+
Hg19::chr12:49741821..49741836,+p@chr12:49741821..49741836
+
Hg19::chr20:60987744..60987756,-p@chr20:60987744..60987756
-
Hg19::chr3:149192427..149192438,+p2@TM4SF4
Hg19::chr7:155754002..155754015,+p@chr7:155754002..155754015
+
Hg19::chr7:155754027..155754046,+p@chr7:155754027..155754046
+
Hg19::chr7:15707836..15707857,+p1@ENST00000451240
p1@uc003ste.2
Hg19::chr7:44580861..44580912,-p1@NPC1L1
Hg19::chr7:44580918..44580934,-p2@NPC1L1
Hg19::chr9:130877633..130877641,-p@chr9:130877633..130877641
-


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:0030299cholesterol absorption0.0135790157865837
GO:0044241lipid digestion0.0135790157865837
GO:0050892intestinal absorption0.0135790157865837
GO:0008158hedgehog receptor activity0.0135790157865837
GO:0015918sterol transport0.0135790157865837
GO:0030301cholesterol transport0.0135790157865837
GO:0022600digestive system process0.0135790157865837
GO:0006695cholesterol biosynthetic process0.0156323542899154
GO:0016126sterol biosynthetic process0.01833980188362
GO:0006487protein amino acid N-linked glycosylation0.0249859883709692
GO:0016324apical plasma membrane0.0249859883709692
GO:0044459plasma membrane part0.0249859883709692
GO:0008203cholesterol metabolic process0.0249859883709692
GO:0042157lipoprotein metabolic process0.0249859883709692
GO:0045177apical part of cell0.0249859883709692
GO:0009058biosynthetic process0.0249859883709692
GO:0006694steroid biosynthetic process0.0249859883709692
GO:0016125sterol metabolic process0.0249859883709692
GO:0007586digestion0.0249859883709692
GO:0030659cytoplasmic vesicle membrane0.0254574086141063
GO:0044433cytoplasmic vesicle part0.0254574086141063
GO:0012506vesicle membrane0.0256606148778984
GO:0006869lipid transport0.0293140852477049
GO:0006486protein amino acid glycosylation0.0349355291417189
GO:0043413biopolymer glycosylation0.0349355291417189
GO:0009101glycoprotein biosynthetic process0.0349355291417189
GO:0009100glycoprotein metabolic process0.0374071710405309
GO:0005886plasma membrane0.0374071710405309
GO:0008202steroid metabolic process0.0374071710405309
GO:0008285negative regulation of cell proliferation0.0374071710405309



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
kidney tubule cell4.62e-1012
nephron tubule epithelial cell4.62e-1012
metabolising cell1.24e-0812
endopolyploid cell1.24e-0812
parenchymal cell1.24e-0812
polyploid cell1.24e-0812
hepatocyte1.24e-0812
kidney cell1.80e-0818
kidney epithelial cell1.80e-0818
epithelial cell of nephron3.15e-0816
Uber Anatomy
Ontology termp-valuen
abdomen element4.04e-1755
abdominal segment element4.04e-1755
abdominal segment of trunk2.53e-1461
abdomen2.53e-1461
trunk region element3.39e-13107
subdivision of digestive tract2.58e-11129
endodermal part of digestive tract2.58e-11129
gastrointestinal system7.77e-1135
digestive tract diverticulum1.08e-1023
cavitated compound organ1.31e-1032
immaterial anatomical entity4.28e-10126
sac4.55e-1026
renal tubule4.62e-1012
nephron tubule4.62e-1012
nephron tubule epithelium4.62e-1012
hepatic diverticulum8.37e-1022
liver primordium8.37e-1022
kidney9.33e-1027
kidney mesenchyme9.33e-1027
kidney rudiment9.33e-1027
kidney field9.33e-1027
epithelium of foregut-midgut junction1.41e-0925
anatomical boundary1.41e-0925
hepatobiliary system1.41e-0925
foregut-midgut junction1.41e-0925
septum transversum1.41e-0925
immune organ2.19e-0926
epithelial sac3.16e-0925
intraembryonic coelom3.20e-0921
excretory tube3.81e-0917
mesonephric epithelium3.81e-0917
mesonephric tubule3.81e-0917
nephric duct3.81e-0917
kidney epithelium3.81e-0917
renal duct3.81e-0917
mesonephric duct3.81e-0917
pronephric duct3.81e-0917
renal system8.78e-0945
intestine1.20e-0827
liver1.27e-0819
digestive gland1.27e-0819
liver bud1.27e-0819
digestive system1.30e-08155
digestive tract1.30e-08155
primitive gut1.30e-08155
gut epithelium1.43e-0854
mesonephros1.95e-0818
pronephros1.95e-0818
nephrogenic cord1.95e-0818
pronephric mesoderm1.95e-0818
rostral part of nephrogenic cord1.95e-0818
presumptive pronephric mesoderm1.95e-0818
nephron epithelium3.15e-0816
nephron3.15e-0816
uriniferous tubule3.15e-0816
metanephric mesenchyme3.15e-0816
nephrogenic mesenchyme3.15e-0816
urinary system structure3.52e-0844
body cavity precursor8.98e-0863
subdivision of trunk1.04e-07113
mixed endoderm/mesoderm-derived structure1.27e-07130
intermediate mesoderm1.31e-0737
adult organism1.56e-07115
mesenchyme2.75e-07238
entire embryonic mesenchyme2.75e-07238
urogenital ridge3.06e-0720
compound organ3.70e-0769
endocrine system5.15e-0745
duct5.92e-0726
endoderm-derived structure9.13e-07169
endoderm9.13e-07169
presumptive endoderm9.13e-07169
Disease
Ontology termp-valuen
adenocarcinoma6.42e-0725


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
EP300#203353.38697086311160.009216261698114180.0348391905128618
FOSL2#235546.772080241824680.001913955163860850.0112608621124705
HNF4A#3172511.56614518147683.16474693899284e-050.00063549895320414
HNF4G#3174411.50136901057870.0002593045920322360.00278129940302503
MAFF#23764211.2630712979890.01290318508912210.0464064102594036
SREBF2#6721287.38865248226950.0002323059271552280.00255306731833788



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.