Coexpression cluster:C336

Full id: C336_left_heart_skeletal_breast_lung_mature_adipose

Phase1 CAGE Peaks

Hg19::chr10:21112200..21112221,-	p@chr10:21112200..21112221 -
Hg19::chr11:111781125..111781137,-	p@chr11:111781125..111781137 -
Hg19::chr12:111348835..111348847,-	p@chr12:111348835..111348847 -
Hg19::chr12:56091538..56091540,-	p@chr12:56091538..56091540 -
Hg19::chr14:23886391..23886400,-	p@chr14:23886391..23886400 -
Hg19::chr14:23893155..23893171,-	p7@MYH7
Hg19::chr15:36887069..36887086,+	p3@C15orf41
Hg19::chr15:63353097..63353109,+	p16@TPM1
Hg19::chr19:2273037..2273052,+	p@chr19:2273037..2273052 +
Hg19::chr1:145441220..145441237,+	p@chr1:145441220..145441237 +
Hg19::chr1:145441715..145441724,+	p@chr1:145441715..145441724 +
Hg19::chr1:16342059..16342090,+	p@chr1:16342059..16342090 +
Hg19::chr20:62120363..62120378,-	p@chr20:62120363..62120378 -
Hg19::chr22:36003307..36003317,-	p@chr22:36003307..36003317 -
Hg19::chr2:26467557..26467568,-	p3@HADHA
Hg19::chr2:26467825..26467841,+	p2@HADHB
Hg19::chr3:37061825..37061832,+	p@chr3:37061825..37061832 +
Hg19::chr3:46902281..46902288,-	p@chr3:46902281..46902288 -
Hg19::chr3:96337038..96337083,-	p@chr3:96337038..96337083 -
Hg19::chr4:186066197..186066221,+	p@chr4:186066197..186066221 +
Hg19::chr5:79030927..79030935,+	p49@CMYA5
Hg19::chr5:79946820..79946857,-	p2@MTRNR2L2
Hg19::chr5:80555040..80555044,+	p@chr5:80555040..80555044 +
Hg19::chr6:123760865..123760870,+	p5@ENST00000427828 p5@ENST00000434768
Hg19::chr6:140400645..140400650,+	p@chr6:140400645..140400650 +
Hg19::chr6:56323932..56323936,-	p67@DST
Hg19::chr7:148638575..148638586,+	p2@RNY5
Hg19::chr7:32110543..32110557,-	p11@PDE1C
Hg19::chr7:80231530..80231551,+	p8@CD36
Hg19::chr7:80231563..80231585,+	p6@CD36
Hg19::chr7:80231609..80231627,+	p11@CD36
Hg19::chr7:95221375..95221386,-	p@chr7:95221375..95221386 -
Hg19::chr8:23584449..23584459,-	p@chr8:23584449..23584459 -
Hg19::chrX:5225192..5225203,-	p1@ENST00000434972

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
3.08914508387101e-06	0.00195542883809035	2	8	Fatty acid elongation in mitochondria (KEGG):00062
0.000103669183166052	0.0164056482360278	2	44	Fatty acid metabolism (KEGG):00071
0.000103669183166052	0.0164056482360278	2	44	Valine, leucine and isoleucine degradation (KEGG):00280
0.000318679660048518	0.0390577663331827	2	77	Cardiac muscle contraction (KEGG):04260
0.000370215794627324	0.0390577663331827	2	83	Hypertrophic cardiomyopathy (HCM) (KEGG):05410
0.000435138292981747	0.0393489342082066	2	90	Dilated cardiomyopathy (KEGG):05414
6.15932363774147e-05	0.0164056482360278	2	34	Fatty Acid Beta Oxidation (Wikipathways):WP143

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:0003988	acetyl-CoA C-acyltransferase activity	6.92129505418527e-05
GO:0004300	enoyl-CoA hydratase activity	6.92129505418527e-05
GO:0003857	3-hydroxyacyl-CoA dehydrogenase activity	6.92129505418527e-05
GO:0016408	C-acyltransferase activity	0.000228214532956531
GO:0006635	fatty acid beta-oxidation	0.00052500760191928
GO:0006631	fatty acid metabolic process	0.000530362812756355
GO:0019395	fatty acid oxidation	0.000800337080983666
GO:0032787	monocarboxylic acid metabolic process	0.00118596621311143
GO:0008016	regulation of heart contraction	0.00118596621311143
GO:0008307	structural constituent of muscle	0.00118596621311143
GO:0003015	heart process	0.00119419938607684
GO:0060047	heart contraction	0.00119419938607684
GO:0030017	sarcomere	0.00119419938607684
GO:0030016	myofibril	0.00135373569175321
GO:0044449	contractile fiber part	0.00162135059197157
GO:0043292	contractile fiber	0.00173032124461943
GO:0003779	actin binding	0.00220390170700477
GO:0016836	hydro-lyase activity	0.00280062572538729
GO:0016508	long-chain-enoyl-CoA hydratase activity	0.00280062572538729
GO:0016507	fatty acid beta-oxidation multienzyme complex	0.00280062572538729
GO:0016509	long-chain-3-hydroxyacyl-CoA dehydrogenase activity	0.00280062572538729
GO:0016835	carbon-oxygen lyase activity	0.00313629135527366
GO:0008092	cytoskeletal protein binding	0.00416575764242442
GO:0005516	calmodulin binding	0.00509004928055831
GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	0.00509004928055831
GO:0008015	blood circulation	0.00509004928055831
GO:0003013	circulatory system process	0.00509004928055831
GO:0006200	ATP catabolic process	0.00509004928055831
GO:0009207	purine ribonucleoside triphosphate catabolic process	0.00509004928055831
GO:0009146	purine nucleoside triphosphate catabolic process	0.00509004928055831
GO:0004117	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity	0.00509004928055831
GO:0003985	acetyl-CoA C-acetyltransferase activity	0.00509004928055831
GO:0009203	ribonucleoside triphosphate catabolic process	0.00509004928055831
GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	0.00509004928055831
GO:0003012	muscle system process	0.00509004928055831
GO:0006936	muscle contraction	0.00509004928055831
GO:0044255	cellular lipid metabolic process	0.00523876299108885
GO:0019752	carboxylic acid metabolic process	0.00534476070800211
GO:0006082	organic acid metabolic process	0.00534476070800211
GO:0009154	purine ribonucleotide catabolic process	0.00534476070800211
GO:0009143	nucleoside triphosphate catabolic process	0.00534476070800211
GO:0006195	purine nucleotide catabolic process	0.00534476070800211
GO:0005862	muscle thin filament tropomyosin	0.00534476070800211
GO:0030898	actin-dependent ATPase activity	0.00534476070800211
GO:0016453	C-acetyltransferase activity	0.00625377080234083
GO:0033275	actin-myosin filament sliding	0.00625377080234083
GO:0030049	muscle filament sliding	0.00625377080234083
GO:0009261	ribonucleotide catabolic process	0.00707946691661464
GO:0002027	regulation of heart rate	0.00707946691661464
GO:0006629	lipid metabolic process	0.00707946691661464
GO:0055010	ventricular cardiac muscle morphogenesis	0.00777643195140338
GO:0007512	adult heart development	0.00777643195140338
GO:0008415	acyltransferase activity	0.00777643195140338
GO:0016747	transferase activity, transferring groups other than amino-acyl groups	0.00777643195140338
GO:0005515	protein binding	0.00788231127580342
GO:0048644	muscle morphogenesis	0.00824767501883972
GO:0055008	cardiac muscle morphogensis	0.00824767501883972
GO:0051239	regulation of multicellular organismal process	0.0087020181146306
GO:0016829	lyase activity	0.0087020181146306
GO:0015629	actin cytoskeleton	0.00952041531412415
GO:0016746	transferase activity, transferring acyl groups	0.00952041531412415
GO:0005865	striated muscle thin filament	0.01028524455451
GO:0005743	mitochondrial inner membrane	0.01028524455451
GO:0019866	organelle inner membrane	0.0112964660841367
GO:0045104	intermediate filament cytoskeleton organization and biogenesis	0.012648071284402
GO:0045103	intermediate filament-based process	0.0131454347830111
GO:0000146	microfilament motor activity	0.0131454347830111
GO:0030048	actin filament-based movement	0.0134192831021231
GO:0032982	myosin filament	0.0134192831021231
GO:0005863	striated muscle thick filament	0.0134192831021231
GO:0031966	mitochondrial membrane	0.0153170358144426
GO:0005856	cytoskeleton	0.0155226771801919
GO:0000062	acyl-CoA binding	0.0160771851772659
GO:0005740	mitochondrial envelope	0.016423777393706
GO:0005859	muscle myosin complex	0.0192918421568587
GO:0009166	nucleotide catabolic process	0.0192918421568587
GO:0016460	myosin II complex	0.0198006200548218
GO:0000302	response to reactive oxygen species	0.0202961757118159
GO:0005504	fatty acid binding	0.0229972128803536
GO:0006941	striated muscle contraction	0.0269794578053047
GO:0044429	mitochondrial part	0.0269794578053047
GO:0042221	response to chemical stimulus	0.0269794578053047
GO:0006937	regulation of muscle contraction	0.0275117531679227
GO:0031967	organelle envelope	0.0290746276768742
GO:0031975	envelope	0.0290746276768742
GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	0.0306153492651917
GO:0004112	cyclic-nucleotide phosphodiesterase activity	0.0316010541811552
GO:0007010	cytoskeleton organization and biogenesis	0.0336575397112977
GO:0044446	intracellular organelle part	0.0404207849669413
GO:0044422	organelle part	0.0404207849669413
GO:0042493	response to drug	0.0404207849669413
GO:0051287	NAD binding	0.0456447248263079

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	4.21e-09	15

Uber Anatomy

Ontology term	p-value	n
adult organism	1.01e-30	115
neural tube	9.01e-14	57
neural rod	9.01e-14	57
future spinal cord	9.01e-14	57
neural keel	9.01e-14	57
regional part of brain	4.92e-11	59
anterior neural tube	6.46e-11	42
gray matter	1.61e-10	34
brain grey matter	1.61e-10	34
regional part of forebrain	2.24e-10	41
forebrain	2.24e-10	41
future forebrain	2.24e-10	41
telencephalon	6.27e-10	34
central nervous system	6.72e-10	82
regional part of telencephalon	7.15e-10	33
brain	3.93e-09	69
future brain	3.93e-09	69
cerebral hemisphere	4.56e-09	32
regional part of nervous system	2.61e-08	94
nervous system	2.61e-08	94
multi-cellular organism	3.76e-08	659
regional part of cerebral cortex	1.20e-07	22
anatomical conduit	2.42e-07	241
organ	7.67e-07	511
cerebral cortex	7.92e-07	25
pallium	7.92e-07	25

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	28.4611949491839	0.00228776074824822	0.0129839933043308

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.