Coexpression cluster:C3540

Full id: C3540_skeletal_left_heart_Mesenchymal_diaphragm_Alveolar_tongue

Phase1 CAGE Peaks

Hg19::chr16:2009500..2009584,+	p1@NDUFB10
Hg19::chr2:98262497..98262549,+	p1@COX5B
Hg19::chr3:48647059..48647102,-	p1@UQCRC1

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
9.66492387457841e-08	1.52947420315203e-05	3	132	Oxidative phosphorylation (KEGG):00190
6.31961929821581e-05	0.00444479890641179	3	1138	Metabolic pathways (KEGG):01100
2.15074464693702e-05	0.00170177670188892	2	77	Cardiac muscle contraction (KEGG):04260
1.96661053766193e-07	2.48972894068001e-05	3	167	Alzheimer's disease (KEGG):05010
9.22896270049956e-08	1.52947420315203e-05	3	130	Parkinson's disease (KEGG):05012
2.59185625084851e-07	2.73440834464518e-05	3	183	Huntington's disease (KEGG):05016
5.41556645674944e-08	1.52947420315203e-05	3	109	Electron Transport Chain (Wikipathways):WP111
2.20095901611869e-08	1.39320705720313e-05	3	81	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. (Reactome):REACT_6305
3.42164256458367e-06	0.000309414249054495	2	31	{CYCS,35} (Static Module):NA

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:0005743	mitochondrial inner membrane	3.94167936296023e-05
GO:0019866	organelle inner membrane	3.94167936296023e-05
GO:0031966	mitochondrial membrane	4.39079275427809e-05
GO:0005740	mitochondrial envelope	4.39079275427809e-05
GO:0044429	mitochondrial part	7.57771798962151e-05
GO:0031967	organelle envelope	7.57771798962151e-05
GO:0031975	envelope	7.57771798962151e-05
GO:0006118	electron transport	0.000104063478946275
GO:0005746	mitochondrial respiratory chain	0.000141381126508339
GO:0006091	generation of precursor metabolites and energy	0.000180464480492059
GO:0005739	mitochondrion	0.000198827660296956
GO:0044455	mitochondrial membrane part	0.000269873470898099
GO:0006119	oxidative phosphorylation	0.000430686169885607
GO:0031090	organelle membrane	0.00053948090000896
GO:0016491	oxidoreductase activity	0.000549886679035116
GO:0015078	hydrogen ion transmembrane transporter activity	0.000570691170457736
GO:0015077	monovalent inorganic cation transmembrane transporter activity	0.000619459136717262
GO:0022890	inorganic cation transmembrane transporter activity	0.000924073405410639
GO:0044446	intracellular organelle part	0.00772108058328133
GO:0044422	organelle part	0.00772108058328133
GO:0008324	cation transmembrane transporter activity	0.00792935597784679
GO:0016681	oxidoreductase activity, acting on diphenols and related substances as donors, cytochrome as acceptor	0.00822131044074366
GO:0008121	ubiquinol-cytochrome-c reductase activity	0.00822131044074366
GO:0016679	oxidoreductase activity, acting on diphenols and related substances as donors	0.00822131044074366
GO:0044444	cytoplasmic part	0.00846379679961598
GO:0007585	respiratory gaseous exchange	0.00846379679961598
GO:0045271	respiratory chain complex I	0.0103427143324249
GO:0030964	NADH dehydrogenase complex (quinone)	0.0103427143324249
GO:0005747	mitochondrial respiratory chain complex I	0.0103427143324249
GO:0004129	cytochrome-c oxidase activity	0.0103427143324249
GO:0016675	oxidoreductase activity, acting on heme group of donors	0.0103427143324249
GO:0016676	oxidoreductase activity, acting on heme group of donors, oxygen as acceptor	0.0103427143324249
GO:0015002	heme-copper terminal oxidase activity	0.0103427143324249
GO:0015075	ion transmembrane transporter activity	0.0110499762773029
GO:0009060	aerobic respiration	0.0110499762773029
GO:0006120	mitochondrial electron transport, NADH to ubiquinone	0.0113739705753752
GO:0016310	phosphorylation	0.0114123006757427
GO:0045333	cellular respiration	0.0115721504980818
GO:0022891	substrate-specific transmembrane transporter activity	0.0128118673586426
GO:0008137	NADH dehydrogenase (ubiquinone) activity	0.0128118673586426
GO:0003954	NADH dehydrogenase activity	0.0128118673586426
GO:0050136	NADH dehydrogenase (quinone) activity	0.0128118673586426
GO:0042775	organelle ATP synthesis coupled electron transport	0.0128469912276672
GO:0016655	oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor	0.0128469912276672
GO:0022857	transmembrane transporter activity	0.0128469912276672
GO:0042773	ATP synthesis coupled electron transport	0.0128484456315034
GO:0006793	phosphorus metabolic process	0.0129587858695853
GO:0006796	phosphate metabolic process	0.0129587858695853
GO:0022892	substrate-specific transporter activity	0.013728668980004
GO:0016651	oxidoreductase activity, acting on NADH or NADPH	0.016352482504285
GO:0015980	energy derivation by oxidation of organic compounds	0.017363226964559
GO:0005737	cytoplasm	0.0176623737467382
GO:0004222	metalloendopeptidase activity	0.0274222150223631
GO:0043231	intracellular membrane-bound organelle	0.0274222150223631
GO:0043227	membrane-bound organelle	0.0274222150223631
GO:0009055	electron carrier activity	0.0340569250592044
GO:0016020	membrane	0.0356268822602444
GO:0043229	intracellular organelle	0.0464093602139209
GO:0043226	organelle	0.0464093602139209
GO:0008237	metallopeptidase activity	0.0471924897371985

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
embryonic cell	2.04e-10	248
contractile cell	7.66e-10	59
electrically responsive cell	1.90e-08	60
electrically active cell	1.90e-08	60
muscle cell	7.91e-08	54
epithelial cell	1.27e-07	254
muscle precursor cell	2.56e-07	57
myoblast	2.56e-07	57
multi-potent skeletal muscle stem cell	2.56e-07	57
mesodermal cell	3.24e-07	119
smooth muscle cell	5.11e-07	42
smooth muscle myoblast	5.11e-07	42

Uber Anatomy

Ontology term	p-value	n
multi-tissue structure	4.76e-19	347
mesenchyme	1.02e-14	238
entire embryonic mesenchyme	1.02e-14	238
epithelium	8.35e-12	309
trunk mesenchyme	1.40e-11	143
cell layer	1.44e-11	312
dermomyotome	4.56e-11	70
organism subdivision	1.02e-10	365
somite	1.22e-10	83
paraxial mesoderm	1.22e-10	83
presomitic mesoderm	1.22e-10	83
presumptive segmental plate	1.22e-10	83
trunk paraxial mesoderm	1.22e-10	83
presumptive paraxial mesoderm	1.22e-10	83
trunk	1.36e-10	216
multilaminar epithelium	2.63e-10	82
organ part	1.59e-09	219
muscle tissue	3.75e-09	63
musculature	3.75e-09	63
musculature of body	3.75e-09	63
skeletal muscle tissue	4.29e-09	61
striated muscle tissue	4.29e-09	61
myotome	4.29e-09	61
epithelial tube	8.99e-09	118
compound organ	1.10e-08	69
tube	1.51e-08	194
embryo	6.61e-08	612
anatomical cluster	1.67e-07	286
germ layer	2.38e-07	604
embryonic tissue	2.38e-07	604
presumptive structure	2.38e-07	604
epiblast (generic)	2.38e-07	604
embryonic structure	2.53e-07	605
developing anatomical structure	2.53e-07	605
anatomical conduit	3.98e-07	241

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
CTCFL#140690	2	13.1643162393162	0.00743336703699601	0.0306754156779211
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324694781804275
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321507180643085
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.031998918599741
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0461316727954534
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00761152113762452
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269213988173359
NR3C1#2908	2	9.98201555411536	0.0127847436554717	0.0460343334816001
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00470547164388949
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172679465127204
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276116509777606
SMC3#9126	2	10.0299552299552	0.012665637976747	0.0457300202120404
STAT1#6772	2	13.8043916647995	0.00677093170844408	0.0287494140219617
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.0054185026445323
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328728570954589

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.