Coexpression cluster:C3631

Full id: C3631_signet_liver_Hepatocyte_lung_gastrointestinal_duodenum_gall

Phase1 CAGE Peaks

Hg19::chr17:39928985..39929000,-	p16@JUP
Hg19::chr3:149193560..149193572,+	p3@TM4SF4
Hg19::chr3:149193636..149193643,+	p10@TM4SF4

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

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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

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GO ID	GO name	FDR corrected p-value
GO:0005916	fascia adherens	0.00800506168636512
GO:0009898	internal side of plasma membrane	0.00800506168636512
GO:0005624	membrane fraction	0.00800506168636512
GO:0030057	desmosome	0.00800506168636512
GO:0000267	cell fraction	0.00800506168636512
GO:0005913	cell-cell adherens junction	0.00800506168636512
GO:0030018	Z disc	0.00800506168636512
GO:0031674	I band	0.00850500241229507
GO:0014704	intercalated disc	0.0166161071869071
GO:0030017	sarcomere	0.0166161071869071
GO:0030016	myofibril	0.0166161071869071
GO:0006487	protein amino acid N-linked glycosylation	0.0166161071869071
GO:0005912	adherens junction	0.0166161071869071
GO:0044449	contractile fiber part	0.0170648948467576
GO:0043292	contractile fiber	0.0170648948467576
GO:0044459	plasma membrane part	0.0192194868159395
GO:0043296	apical junction complex	0.0233168186805186
GO:0016327	apicolateral plasma membrane	0.0233168186805186
GO:0005911	intercellular junction	0.0330299548248979
GO:0006486	protein amino acid glycosylation	0.0330299548248979
GO:0043413	biopolymer glycosylation	0.0330299548248979
GO:0009101	glycoprotein biosynthetic process	0.0330299548248979
GO:0009100	glycoprotein metabolic process	0.0357413648296294
GO:0005886	plasma membrane	0.0357413648296294
GO:0008285	negative regulation of cell proliferation	0.0359061114950822
GO:0005625	soluble fraction	0.0359061114950822
GO:0015629	actin cytoskeleton	0.0436974359223854
GO:0016337	cell-cell adhesion	0.0493596312651508

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>

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Cell Type

Ontology term	p-value	n
metabolising cell	2.95e-17	12
endopolyploid cell	2.95e-17	12
parenchymal cell	2.95e-17	12
polyploid cell	2.95e-17	12
hepatocyte	2.95e-17	12

Uber Anatomy

Ontology term	p-value	n
epithelium of foregut-midgut junction	1.58e-20	25
anatomical boundary	1.58e-20	25
hepatobiliary system	1.58e-20	25
foregut-midgut junction	1.58e-20	25
septum transversum	1.58e-20	25
epithelial sac	2.85e-20	25
hepatic diverticulum	4.33e-20	22
liver primordium	4.33e-20	22
liver	7.66e-20	19
digestive gland	7.66e-20	19
liver bud	7.66e-20	19
sac	2.29e-19	26
digestive tract diverticulum	4.34e-19	23
gut epithelium	1.63e-17	54
endo-epithelium	6.95e-17	82
immune organ	2.94e-16	26
endocrine gland	2.24e-13	35
subdivision of digestive tract	1.83e-12	129
endodermal part of digestive tract	1.83e-12	129
digestive system	4.14e-12	155
digestive tract	4.14e-12	155
primitive gut	4.14e-12	155
abdomen element	1.48e-11	55
abdominal segment element	1.48e-11	55
abdominal segment of trunk	1.70e-11	61
abdomen	1.70e-11	61
endocrine system	1.83e-11	45
endoderm-derived structure	2.13e-11	169
endoderm	2.13e-11	169
presumptive endoderm	2.13e-11	169
exocrine gland	3.55e-11	31
exocrine system	3.55e-11	31
mixed endoderm/mesoderm-derived structure	2.27e-09	130
gland	3.99e-09	59
foregut	1.71e-08	98
trunk region element	2.87e-08	107
subdivision of trunk	1.57e-07	113
immaterial anatomical entity	3.44e-07	126
gastrointestinal system	7.62e-07	35

Disease

Ontology term	p-value	n
clear cell adenocarcinoma	5.78e-08	2
carcinoma	1.84e-07	106

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

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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

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

TF	#promoters	Enrichment	p-value	q-value
ESRRA#2101	1	161.280104712042	0.00618762008021956	0.0273489717532714

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

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This analysis result is provided for C0 - C305 clusters.