Coexpression cluster:C3765

Full id: C3765_amniotic_colon_Alveolar_duodenum_small_mucinous_stomach

Phase1 CAGE Peaks

Hg19::chr19:17905594..17905645,+	p2@B3GNT3
Hg19::chr3:38032245..38032254,+	p9@VILL
Hg19::chr3:38032261..38032292,+	p2@VILL

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:0051693	actin filament capping	0.0200002805393231
GO:0051016	barbed-end actin filament capping	0.0200002805393231
GO:0030835	negative regulation of actin filament depolymerization	0.0200002805393231
GO:0030834	regulation of actin filament depolymerization	0.0200002805393231
GO:0030042	actin filament depolymerization	0.0200002805393231
GO:0008378	galactosyltransferase activity	0.0200002805393231
GO:0008064	regulation of actin polymerization and/or depolymerization	0.0200002805393231
GO:0051261	protein depolymerization	0.0200002805393231
GO:0030832	regulation of actin filament length	0.0200002805393231
GO:0032535	regulation of cellular component size	0.0200002805393231
GO:0032956	regulation of actin cytoskeleton organization and biogenesis	0.0200002805393231
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0200002805393231
GO:0051493	regulation of cytoskeleton organization and biogenesis	0.0200002805393231
GO:0033043	regulation of organelle organization and biogenesis	0.0200002805393231
GO:0008154	actin polymerization and/or depolymerization	0.0203321209406293
GO:0005200	structural constituent of cytoskeleton	0.0265515254511121
GO:0051128	regulation of cellular component organization and biogenesis	0.0288688677256041
GO:0051248	negative regulation of protein metabolic process	0.0288688677256041
GO:0006486	protein amino acid glycosylation	0.0432535122706996
GO:0043413	biopolymer glycosylation	0.0432535122706996
GO:0009101	glycoprotein biosynthetic process	0.0432535122706996
GO:0009100	glycoprotein metabolic process	0.0471675445434154

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
epithelial cell	8.00e-23	254
endodermal cell	1.62e-16	59
endo-epithelial cell	6.60e-16	43
respiratory epithelial cell	3.00e-09	13
epithelial cell of alimentary canal	1.07e-07	21

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	2.54e-35	169
endoderm	2.54e-35	169
presumptive endoderm	2.54e-35	169
digestive system	1.02e-29	155
digestive tract	1.02e-29	155
primitive gut	1.02e-29	155
subdivision of digestive tract	1.03e-29	129
endodermal part of digestive tract	1.03e-29	129
mixed endoderm/mesoderm-derived structure	1.01e-25	130
foregut	4.61e-20	98
respiratory system	2.02e-17	72
respiratory tract	7.25e-17	53
endo-epithelium	4.51e-15	82
respiratory primordium	2.32e-13	38
endoderm of foregut	2.32e-13	38
segment of respiratory tract	9.30e-12	46
immaterial anatomical entity	4.77e-11	126
trunk region element	8.31e-11	107
mesenchyme	4.72e-10	238
entire embryonic mesenchyme	4.72e-10	238
gastrointestinal system	4.76e-10	35
anatomical space	2.89e-09	104
thoracic cavity element	3.58e-09	34
thoracic cavity	3.58e-09	34
thoracic segment organ	1.00e-08	35
intestine	3.52e-08	27
lung	6.67e-08	22
respiratory tube	6.67e-08	22
respiration organ	6.67e-08	22
pair of lungs	6.67e-08	22
lung primordium	6.67e-08	22
lung bud	6.67e-08	22
epithelial bud	7.32e-08	37
gut epithelium	7.43e-07	54
orifice	7.78e-07	35
multi-tissue structure	7.89e-07	347

Disease

Ontology term	p-value	n
carcinoma	1.14e-22	106
cell type cancer	6.94e-15	143
adenocarcinoma	1.41e-11	25
squamous cell carcinoma	1.73e-07	14
cancer	2.60e-07	235
disease of cellular proliferation	8.99e-07	239

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279398069079786

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.