Coexpression cluster:C1157

Full id: C1157_Hepatic_neuroectodermal_liver_Hepatocyte_Adipocyte_spleen_kidney

Phase1 CAGE Peaks

Hg19::chr11:940729..940745,+	p5@AP2A2
Hg19::chr19:7861495..7861500,+	p@chr19:7861495..7861500 +
Hg19::chr3:58196639..58196653,-	p2@DNASE1L3
Hg19::chr3:58196655..58196668,-	p3@DNASE1L3
Hg19::chr3:58196822..58196832,-	p9@DNASE1L3
Hg19::chr3:58196939..58196956,-	p7@DNASE1L3
Hg19::chr7:158330204..158330217,+	p2@ENST00000448698

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:0030128	clathrin coat of endocytic vesicle	0.00906548923612662
GO:0030669	clathrin-coated endocytic vesicle membrane	0.00906548923612662
GO:0030122	AP-2 adaptor complex	0.00906548923612662
GO:0030666	endocytic vesicle membrane	0.00906548923612662
GO:0045334	clathrin-coated endocytic vesicle	0.00906548923612662
GO:0030132	clathrin coat of coated pit	0.0124081634475196
GO:0006309	DNA fragmentation during apoptosis	0.0124081634475196
GO:0006921	cell structure disassembly during apoptosis	0.0124081634475196
GO:0030139	endocytic vesicle	0.0124081634475196
GO:0030125	clathrin vesicle coat	0.0124081634475196
GO:0030262	apoptotic nuclear changes	0.0124081634475196
GO:0030665	clathrin coated vesicle membrane	0.0124081634475196
GO:0006308	DNA catabolic process	0.0166393790457123
GO:0006997	nuclear organization and biogenesis	0.0166393790457123
GO:0005905	coated pit	0.0166393790457123
GO:0022411	cellular component disassembly	0.0166393790457123
GO:0030120	vesicle coat	0.0166393790457123
GO:0004536	deoxyribonuclease activity	0.0166393790457123
GO:0030662	coated vesicle membrane	0.0166393790457123
GO:0030131	clathrin adaptor complex	0.0166393790457123
GO:0030119	AP-type membrane coat adaptor complex	0.0166393790457123
GO:0030118	clathrin coat	0.0194091775309714
GO:0008632	apoptotic program	0.0250265430168767
GO:0030659	cytoplasmic vesicle membrane	0.0258598402874453
GO:0044433	cytoplasmic vesicle part	0.0258598402874453
GO:0012506	vesicle membrane	0.0258598402874453
GO:0030136	clathrin-coated vesicle	0.0258598402874453
GO:0030117	membrane coat	0.0258598402874453
GO:0048475	coated membrane	0.0258598402874453
GO:0030135	coated vesicle	0.0310077056707032
GO:0004519	endonuclease activity	0.0310077056707032
GO:0008565	protein transporter activity	0.0310077056707032
GO:0016043	cellular component organization and biogenesis	0.0310077056707032
GO:0010324	membrane invagination	0.0363450338784508
GO:0006897	endocytosis	0.0363450338784508
GO:0004518	nuclease activity	0.0440925552788139
GO:0016044	membrane organization and biogenesis	0.0495000262251407

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><br>

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Cell Type

Ontology term	p-value	n
endothelial cell of umbilical vein	9.32e-17	3
vein endothelial cell	1.25e-08	6

Uber Anatomy

Ontology term	p-value	n
spleen	2.12e-17	3
gastrointestinal system mesentery	2.12e-17	3
stomach region	2.12e-17	3
mesentery	2.12e-17	3
gastrointestinal system serosa	2.12e-17	3
mesentery of stomach	2.12e-17	3
gut mesentery	2.12e-17	3
dorsal mesentery	2.12e-17	3
dorsal mesogastrium	2.12e-17	3
peritoneal cavity	2.12e-17	3
spleen primordium	2.12e-17	3
umbilical vein	2.90e-10	5
adult organism	4.54e-10	114
vein	1.06e-09	9
venous blood vessel	1.06e-09	9
venous system	1.06e-09	9
abdomen element	1.20e-08	54
abdominal segment element	1.20e-08	54
mixed endoderm/mesoderm-derived structure	2.16e-08	29
hemopoietic organ	9.99e-08	7
immune organ	9.99e-08	7
intraembryonic coelom	1.19e-07	12
abdominal segment of trunk	1.33e-07	60
abdomen	1.33e-07	60
dura mater	5.26e-07	1
future meninx	5.26e-07	1
ectomeninx	5.26e-07	1
future dura mater	5.26e-07	1
endocrine gland	6.07e-07	35
stomach	8.23e-07	8
food storage organ	8.23e-07	8
mitral valve	9.79e-07	1

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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No analysis results for this cluster

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.