Coexpression cluster:C220

Full id: C220_Adipocyte_mature_left_breast_skin_liver_adipose

Phase1 CAGE Peaks

Hg19::chr10:102107103..102107119,+	p3@SCD
Hg19::chr10:102107865..102107900,-	p@chr10:102107865..102107900 -
Hg19::chr10:102107922..102107940,-	p@chr10:102107922..102107940 -
Hg19::chr10:102107942..102107961,+	p16@SCD
Hg19::chr10:102107962..102107989,-	p@chr10:102107962..102107989 -
Hg19::chr10:102120575..102120608,+	p@chr10:102120575..102120608 +
Hg19::chr10:102120908..102120961,+	p1@ENST00000537595
Hg19::chr10:102121321..102121343,-	p1@AF116616
Hg19::chr11:111895937..111895954,+	p5@DLAT
Hg19::chr11:111895969..111895977,+	p8@DLAT
Hg19::chr11:63273520..63273537,+	p2@LGALS12
Hg19::chr11:63273547..63273624,+	p1@LGALS12
Hg19::chr11:63273633..63273644,+	p3@LGALS12
Hg19::chr11:63273651..63273660,+	p7@LGALS12
Hg19::chr11:63273811..63273822,+	p6@LGALS12
Hg19::chr11:63273968..63273973,+	p12@LGALS12
Hg19::chr11:63381642..63381653,-	p11@PLA2G16
Hg19::chr11:77779210..77779221,+	p@chr11:77779210..77779221 +
Hg19::chr11:821771..821791,+	p6@PNPLA2
Hg19::chr11:821805..821820,+	p4@PNPLA2
Hg19::chr11:821969..822000,+	p9@PNPLA2
Hg19::chr11:822471..822487,+	p8@PNPLA2
Hg19::chr11:823694..823744,+	p5@PNPLA2
Hg19::chr11:823806..823819,+	p19@PNPLA2
Hg19::chr11:824556..824594,+	p@chr11:824556..824594 +
Hg19::chr11:824631..824643,+	p@chr11:824631..824643 +
Hg19::chr11:824728..824765,+	p@chr11:824728..824765 +
Hg19::chr11:824844..824872,+	p@chr11:824844..824872 +
Hg19::chr11:825003..825018,+	p@chr11:825003..825018 +
Hg19::chr12:50503990..50504003,+	p@chr12:50503990..50504003 +
Hg19::chr12:56102486..56102497,-	p@chr12:56102486..56102497 -
Hg19::chr14:74035911..74035922,+	p2@ACOT2
Hg19::chr14:74035970..74036005,+	p1@ACOT2
Hg19::chr15:90233866..90233883,-	p2@PEX11A
Hg19::chr17:17425661..17425669,-	p@chr17:17425661..17425669 -
Hg19::chr17:17480330..17480331,-	p22@PEMT
Hg19::chr17:17480334..17480356,-	p9@PEMT
Hg19::chr17:17480357..17480403,-	p4@PEMT
Hg19::chr17:17480405..17480422,-	p12@PEMT
Hg19::chr17:17480455..17480488,-	p7@PEMT
Hg19::chr17:17480494..17480502,-	p15@PEMT
Hg19::chr17:20687991..20688022,-	p@chr17:20687991..20688022 -
Hg19::chr17:41003302..41003317,+	p3@AOC3
Hg19::chr17:41003393..41003400,+	p2@CU690716
Hg19::chr17:41004526..41004533,-	p@chr17:41004526..41004533 -
Hg19::chr17:41005283..41005312,+	p@chr17:41005283..41005312 +
Hg19::chr17:80049335..80049378,-	p@chr17:80049335..80049378 -
Hg19::chr19:4503940..4503950,-	p@chr19:4503940..4503950 -
Hg19::chr21:33671160..33671172,+	p2@MRAP
Hg19::chr21:33671264..33671281,+	p1@MRAP
Hg19::chr2:176046144..176046189,-	p2@ATP5G3
Hg19::chr2:176046192..176046216,-	p3@ATP5G3
Hg19::chr2:85598470..85598482,+	p@chr2:85598470..85598482 +
Hg19::chr3:12200368..12200494,-	p1@TIMP4
Hg19::chr3:186572519..186572536,+	p@chr3:186572519..186572536 +
Hg19::chr3:9908708..9908727,-	p@chr3:9908708..9908727 -
Hg19::chr5:76382989..76383001,-	p4@ZBED3
Hg19::chr5:76435018..76435030,+	p2@ENST00000511547 p2@ENST00000515356
Hg19::chr6:53187504..53187521,-	p@chr6:53187504..53187521 -
Hg19::chr8:19805751..19805767,+	p@chr8:19805751..19805767 +
Hg19::chr8:82391739..82391754,-	p3@FABP4
Hg19::chr8:82392791..82392838,-	p@chr8:82392791..82392838 -
Hg19::chr9:101673536..101673545,+	p@chr9:101673536..101673545 +
Hg19::chr9:139580642..139580653,-	p@chr9:139580642..139580653 -
Hg19::chrX:2742090..2742104,-	p@chrX:2742090..2742104 -
Hg19::chrX:2742111..2742121,-	p@chrX:2742111..2742121 -

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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p.value	FDR	nGenes	nPathway	Name
4.66554697163602e-05	0.029532912330456	2	21	Biosynthesis of unsaturated fatty acids (KEGG):01040

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:0044444	cytoplasmic part	0.0126663134345932
GO:0032787	monocarboxylic acid metabolic process	0.0126663134345932
GO:0006732	coenzyme metabolic process	0.0126663134345932
GO:0051186	cofactor metabolic process	0.0126663134345932
GO:0006629	lipid metabolic process	0.0126663134345932
GO:0005737	cytoplasm	0.0126663134345932
GO:0030395	lactose binding	0.0126663134345932
GO:0004608	phosphatidylethanolamine N-methyltransferase activity	0.0126663134345932
GO:0005967	mitochondrial pyruvate dehydrogenase complex	0.0126663134345932
GO:0048030	disaccharide binding	0.0126663134345932
GO:0005739	mitochondrion	0.0129812627465017
GO:0045254	pyruvate dehydrogenase complex	0.0211067938244365
GO:0030523	dihydrolipoamide S-acyltransferase activity	0.025323679275354
GO:0006085	acetyl-CoA biosynthetic process	0.025323679275354
GO:0004742	dihydrolipoyllysine-residue acetyltransferase activity	0.025323679275354
GO:0044429	mitochondrial part	0.0266517967653305
GO:0001676	long-chain fatty acid metabolic process	0.0266517967653305
GO:0016418	S-acetyltransferase activity	0.0266517967653305
GO:0004768	stearoyl-CoA 9-desaturase activity	0.0266517967653305
GO:0048038	quinone binding	0.03013658993362
GO:0006656	phosphatidylcholine biosynthetic process	0.03013658993362
GO:0031090	organelle membrane	0.0303578874399766
GO:0004091	carboxylesterase activity	0.0311764867052478
GO:0016559	peroxisome fission	0.0311764867052478
GO:0006631	fatty acid metabolic process	0.0311764867052478
GO:0046470	phosphatidylcholine metabolic process	0.0320330169712323
GO:0008131	amine oxidase activity	0.0320330169712323
GO:0044255	cellular lipid metabolic process	0.0320330169712323
GO:0048285	organelle fission	0.0320330169712323
GO:0016290	palmitoyl-CoA hydrolase activity	0.0320330169712323
GO:0019752	carboxylic acid metabolic process	0.0320330169712323
GO:0006082	organic acid metabolic process	0.0320330169712323
GO:0000038	very-long-chain fatty acid metabolic process	0.0344957177227504
GO:0016417	S-acyltransferase activity	0.0361319901495177
GO:0005811	lipid particle	0.0361319901495177
GO:0031405	lipoic acid binding	0.0366009477120791
GO:0050729	positive regulation of inflammatory response	0.0366009477120791
GO:0031349	positive regulation of defense response	0.0366009477120791
GO:0005783	endoplasmic reticulum	0.0370001895799611
GO:0005753	mitochondrial proton-transporting ATP synthase complex	0.0370001895799611
GO:0016717	oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water	0.0370001895799611
GO:0031406	carboxylic acid binding	0.0397629278746713
GO:0006954	inflammatory response	0.0397629278746713
GO:0042632	cholesterol homeostasis	0.0397629278746713
GO:0055092	sterol homeostasis	0.0397629278746713
GO:0005779	integral to peroxisomal membrane	0.0397629278746713
GO:0031231	intrinsic to peroxisomal membrane	0.0397629278746713
GO:0006637	acyl-CoA metabolic process	0.0397629278746713
GO:0016021	integral to membrane	0.0397629278746713
GO:0008191	metalloendopeptidase inhibitor activity	0.0397629278746713
GO:0004806	triacylglycerol lipase activity	0.0397629278746713
GO:0045263	proton-transporting ATP synthase complex, coupling factor F(o)	0.0397629278746713
GO:0033177	proton-transporting two-sector ATPase complex, proton-transporting domain	0.0397629278746713
GO:0055088	lipid homeostasis	0.0397629278746713
GO:0031224	intrinsic to membrane	0.0399045641103036
GO:0008610	lipid biosynthetic process	0.0407682750111408
GO:0044424	intracellular part	0.0407682750111408
GO:0043231	intracellular membrane-bound organelle	0.0407682750111408
GO:0043227	membrane-bound organelle	0.0407682750111408
GO:0016291	acyl-CoA thioesterase activity	0.0441758179602411
GO:0045259	proton-transporting ATP synthase complex	0.0468057706955094
GO:0016641	oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor	0.0468057706955094
GO:0031347	regulation of defense response	0.0492685748199168
GO:0050727	regulation of inflammatory response	0.0492685748199168

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
fat cell	5.94e-49	15
subcutaneous fat cell	6.13e-17	3
adipocyte of omentum tissue	1.21e-16	3
adipocyte of breast	1.31e-11	2

Uber Anatomy

Ontology term	p-value	n
subcutaneous adipose tissue	6.13e-17	3
adult organism	2.09e-14	114
hypodermis	2.38e-10	5
omentum	1.50e-08	6
peritoneum	1.50e-08	6
abdominal cavity	1.50e-08	6
visceral peritoneum	1.50e-08	6
valve	9.55e-08	3
cardiac mesenchyme	9.55e-08	3
cardial valve	9.55e-08	3
tunica intima	9.55e-08	3
heart layer	9.55e-08	3
endocardium	9.55e-08	3
endocardial cushion	9.55e-08	3
presumptive endocardium	9.55e-08	3

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	2	14.6618277010947	0.00837463940280803	0.032912096503852
HNF4A#3172	8	2.80391398338833	0.0074808357135261	0.0308481462899259

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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