Coexpression cluster:C1752

Full id: C1752_left_heart_diaphragm_tongue_skeletal_nonsmall_chronic

Phase1 CAGE Peaks

Hg19::chr15:75230368..75230470,-	p1@COX5A
Hg19::chr16:23607619..23607645,-	p1@NDUFAB1
Hg19::chr19:29704017..29704086,-	p1@UQCRFS1
Hg19::chr1:17380510..17380541,-	p1@SDHB
Hg19::chr2:176046426..176046445,-	p1@ATP5G3

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
1.95890826360539e-12	4.13329643620737e-10	5	132	Oxidative phosphorylation (KEGG):00190
9.98425842405372e-08	7.90004447803251e-06	5	1138	Metabolic pathways (KEGG):01100
7.14406195160067e-05	0.00452219121536323	2	77	Cardiac muscle contraction (KEGG):04260
6.45306136521003e-12	1.02119696104449e-09	5	167	Alzheimer's disease (KEGG):05010
1.81277180396793e-12	4.13329643620737e-10	5	130	Parkinson's disease (KEGG):05012
1.02506741390146e-11	1.29773534599925e-09	5	183	Huntington's disease (KEGG):05016
7.39869346801531e-13	4.13329643620737e-10	5	109	Electron Transport Chain (Wikipathways):WP111
4.32675276711781e-05	0.00304314944620619	2	60	Oxidative phosphorylation (Wikipathways):WP623
3.00081089502779e-10	3.16585549425432e-08	4	81	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. (Reactome):REACT_6305
1.15784794118768e-08	1.04702535253114e-06	3	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	7.2853062072682e-09
GO:0019866	organelle inner membrane	7.2853062072682e-09
GO:0031966	mitochondrial membrane	1.38927723826689e-08
GO:0005740	mitochondrial envelope	1.38927723826689e-08
GO:0044429	mitochondrial part	5.02766866119338e-08
GO:0031967	organelle envelope	5.02766866119338e-08
GO:0031975	envelope	5.02766866119338e-08
GO:0006091	generation of precursor metabolites and energy	3.39472935653337e-07
GO:0005739	mitochondrion	4.15840126942672e-07
GO:0031090	organelle membrane	2.95776471166315e-06
GO:0044455	mitochondrial membrane part	6.8159481496038e-06
GO:0006118	electron transport	1.44109041859651e-05
GO:0051537	2 iron, 2 sulfur cluster binding	2.07294526011205e-05
GO:0015078	hydrogen ion transmembrane transporter activity	2.5453239825651e-05
GO:0015077	monovalent inorganic cation transmembrane transporter activity	2.94318430339811e-05
GO:0009055	electron carrier activity	4.31458558391117e-05
GO:0022890	inorganic cation transmembrane transporter activity	5.15813345278657e-05
GO:0016491	oxidoreductase activity	0.00020066728170363
GO:0044446	intracellular organelle part	0.000226561805997089
GO:0044422	organelle part	0.000226561805997089
GO:0005506	iron ion binding	0.000256993805734495
GO:0022892	substrate-specific transporter activity	0.000271153402186825
GO:0044444	cytoplasmic part	0.00033485274735131
GO:0005746	mitochondrial respiratory chain	0.000350378200014024
GO:0051536	iron-sulfur cluster binding	0.000454123761373975
GO:0051540	metal cluster binding	0.000454123761373975
GO:0000036	acyl carrier activity	0.000898849472674975
GO:0051538	3 iron, 4 sulfur cluster binding	0.000898849472674975
GO:0008324	cation transmembrane transporter activity	0.000952869621391505
GO:0006119	oxidative phosphorylation	0.00122936405546985
GO:0008177	succinate dehydrogenase (ubiquinone) activity	0.00157289396957018
GO:0016635	oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor	0.00157289396957018
GO:0005737	cytoplasm	0.00268233112191118
GO:0015075	ion transmembrane transporter activity	0.00278155976828436
GO:0005750	mitochondrial respiratory chain complex III	0.00279592670347524
GO:0045275	respiratory chain complex III	0.00279592670347524
GO:0006732	coenzyme metabolic process	0.00325469978139115
GO:0022891	substrate-specific transmembrane transporter activity	0.00376566803596882
GO:0051186	cofactor metabolic process	0.00436798411105563
GO:0022857	transmembrane transporter activity	0.00442111345383874
GO:0043231	intracellular membrane-bound organelle	0.0048177319164742
GO:0043227	membrane-bound organelle	0.0048177319164742
GO:0005753	mitochondrial proton-transporting ATP synthase complex	0.00701902077007293
GO:0016020	membrane	0.00755048581224576
GO:0045263	proton-transporting ATP synthase complex, coupling factor F(o)	0.00929238040428365
GO:0033177	proton-transporting two-sector ATPase complex, proton-transporting domain	0.00929238040428365
GO:0043229	intracellular organelle	0.0113906628961492
GO:0043226	organelle	0.0113906628961492
GO:0045259	proton-transporting ATP synthase complex	0.0117981586232232
GO:0016681	oxidoreductase activity, acting on diphenols and related substances as donors, cytochrome as acceptor	0.0125653841763755
GO:0008121	ubiquinol-cytochrome-c reductase activity	0.0125653841763755
GO:0016679	oxidoreductase activity, acting on diphenols and related substances as donors	0.0125653841763755
GO:0031177	phosphopantetheine binding	0.0128017131677387
GO:0043234	protein complex	0.0168600035498525
GO:0043169	cation binding	0.0168600035498525
GO:0006099	tricarboxylic acid cycle	0.0168600035498525
GO:0051539	4 iron, 4 sulfur cluster binding	0.0168600035498525
GO:0046356	acetyl-CoA catabolic process	0.0168600035498525
GO:0030964	NADH dehydrogenase complex (quinone)	0.0168600035498525
GO:0045271	respiratory chain complex I	0.0168600035498525
GO:0005747	mitochondrial respiratory chain complex I	0.0168600035498525
GO:0006084	acetyl-CoA metabolic process	0.0168600035498525
GO:0004129	cytochrome-c oxidase activity	0.0168600035498525
GO:0009109	coenzyme catabolic process	0.0168600035498525
GO:0016676	oxidoreductase activity, acting on heme group of donors, oxygen as acceptor	0.0168600035498525
GO:0015002	heme-copper terminal oxidase activity	0.0168600035498525
GO:0016675	oxidoreductase activity, acting on heme group of donors	0.0168600035498525
GO:0046872	metal ion binding	0.0173435949224824
GO:0051187	cofactor catabolic process	0.0179616079764488
GO:0043167	ion binding	0.0179616079764488
GO:0009060	aerobic respiration	0.0180251282075584
GO:0006120	mitochondrial electron transport, NADH to ubiquinone	0.0188170305774173
GO:0044424	intracellular part	0.0189038473447777
GO:0045333	cellular respiration	0.0196600140575334
GO:0050136	NADH dehydrogenase (quinone) activity	0.022868458163971
GO:0008137	NADH dehydrogenase (ubiquinone) activity	0.022868458163971
GO:0003954	NADH dehydrogenase activity	0.022868458163971
GO:0006633	fatty acid biosynthetic process	0.022868458163971
GO:0046933	hydrogen ion transporting ATP synthase activity, rotational mechanism	0.022868458163971
GO:0046961	hydrogen ion transporting ATPase activity, rotational mechanism	0.022868458163971
GO:0042775	organelle ATP synthesis coupled electron transport	0.0229192437815628
GO:0016655	oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor	0.0229192437815628
GO:0042773	ATP synthesis coupled electron transport	0.0230985066008147
GO:0015985	energy coupled proton transport, down electrochemical gradient	0.0230985066008147
GO:0015986	ATP synthesis coupled proton transport	0.0230985066008147
GO:0046394	carboxylic acid biosynthetic process	0.0230985066008147
GO:0006754	ATP biosynthetic process	0.0230985066008147
GO:0006753	nucleoside phosphate metabolic process	0.0230985066008147
GO:0016627	oxidoreductase activity, acting on the CH-CH group of donors	0.0230985066008147
GO:0016053	organic acid biosynthetic process	0.0230985066008147
GO:0032991	macromolecular complex	0.0234562649297863
GO:0046034	ATP metabolic process	0.0252954145620041
GO:0019829	cation-transporting ATPase activity	0.0252954145620041
GO:0006810	transport	0.0252954145620041
GO:0051234	establishment of localization	0.0268075628635383
GO:0016310	phosphorylation	0.027561748733795
GO:0016469	proton-transporting two-sector ATPase complex	0.027561748733795
GO:0016651	oxidoreductase activity, acting on NADH or NADPH	0.027561748733795
GO:0005622	intracellular	0.0280800180736992
GO:0015980	energy derivation by oxidation of organic compounds	0.0292458890931553
GO:0009145	purine nucleoside triphosphate biosynthetic process	0.0293578898059736
GO:0009206	purine ribonucleoside triphosphate biosynthetic process	0.0293578898059736
GO:0009201	ribonucleoside triphosphate biosynthetic process	0.0293578898059736
GO:0009142	nucleoside triphosphate biosynthetic process	0.0302681620625602
GO:0051179	localization	0.0303555756583221
GO:0009205	purine ribonucleoside triphosphate metabolic process	0.0305242924512726
GO:0009144	purine nucleoside triphosphate metabolic process	0.0305242924512726
GO:0009199	ribonucleoside triphosphate metabolic process	0.0305242924512726
GO:0015992	proton transport	0.0306450127356899
GO:0006818	hydrogen transport	0.0306450127356899
GO:0006752	group transfer coenzyme metabolic process	0.0310383140586656
GO:0009141	nucleoside triphosphate metabolic process	0.032460169643806
GO:0009152	purine ribonucleotide biosynthetic process	0.032460169643806
GO:0006793	phosphorus metabolic process	0.0334633945678108
GO:0006796	phosphate metabolic process	0.0334633945678108
GO:0009150	purine ribonucleotide metabolic process	0.0334633945678108
GO:0009260	ribonucleotide biosynthetic process	0.0334633945678108
GO:0006164	purine nucleotide biosynthetic process	0.0335985227240659
GO:0046914	transition metal ion binding	0.0343342368163303
GO:0006163	purine nucleotide metabolic process	0.034805727032307
GO:0009259	ribonucleotide metabolic process	0.034805727032307
GO:0006631	fatty acid metabolic process	0.0389637183680753
GO:0009108	coenzyme biosynthetic process	0.0394470093840013
GO:0044249	cellular biosynthetic process	0.0399590195081676
GO:0042625	ATPase activity, coupled to transmembrane movement of ions	0.0411754249305958
GO:0051188	cofactor biosynthetic process	0.043380794214328
GO:0019842	vitamin binding	0.0478595387983076
GO:0009165	nucleotide biosynthetic process	0.0493947362250097

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	8.27e-09	253
embryonic cell	1.69e-07	250

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	1.31e-07	78
mesenchyme	3.94e-07	160
entire embryonic mesenchyme	3.94e-07	160
multi-tissue structure	5.76e-07	342

Disease

Ontology term	p-value	n
hematologic cancer	3.31e-10	51
immune system cancer	3.31e-10	51
leukemia	1.20e-07	39
cancer	2.75e-07	235
disease of cellular proliferation	3.28e-07	239
myeloid leukemia	8.58e-07	31

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
CCNT2#905	4	5.06896126157011	0.00270999809128077	0.0148939373075447
E2F1#1869	5	4.90738921487932	0.000351281809925646	0.00352628997951024
E2F4#1874	4	10.1344482522276	0.000181820150963297	0.0022031691317387
EGR1#1958	4	3.99054327584811	0.006780098300144	0.0287649464341203
ELF1#1997	5	4.25809795880754	0.000714241693977684	0.0057301189335793
EP300#2033	4	5.41915338097856	0.0020938692794389	0.01211599610368
ESRRA#2101	1	96.768062827225	0.0102914705751607	0.0382311622465393
GABPB1#2553	4	5.65414706894574	0.00177669650209667	0.01090738337541
HDAC2#3066	3	8.04937214197576	0.00369167399224669	0.0186258328539252
HEY1#23462	5	4.04011104310571	0.000928885220517799	0.0067411467963073
HMGN3#9324	5	8.17854772335059	2.73180911341838e-05	0.000581666487250361
HNF4G#3174	2	11.5013690105787	0.0112743830492105	0.0413777028947708
IRF1#3659	4	6.10973100285112	0.00131552526476799	0.00880944749468482
MXI1#4601	3	5.97694297725558	0.00865300488936688	0.0329508924976514
MYC#4609	4	4.17782549728752	0.00569196903682344	0.0256776620550647
NANOG#79923	2	11.6979113924051	0.0109116495195608	0.0402202923757115
NR2C2#7182	3	19.5687665431445	0.000275017170096661	0.00293116830571743
NRF1#4899	4	9.76822355816873	0.000210129774810679	0.00244466342335441
PAX5#5079	5	6.66956553117783	7.57493746384605e-05	0.00116994808309172
POU2F2#5452	3	5.46367443464551	0.0111565009446978	0.0410113618726299
PPARGC1A#10891	1	70.0102272727273	0.0142024041946422	0.0498197995393223
RXRA#6256	3	12.04477028348	0.00114526216283683	0.00783506059377152
SIN3A#25942	4	4.32710778145211	0.00497705285576288	0.0232426409945904
SP1#6667	4	4.55870510251272	0.0040757356578168	0.0194839454555192
SP2#6668	2	10.4614121975379	0.0135319118334714	0.0477807606997065
SRF#6722	3	8.27830695730069	0.00340484607377615	0.0173589806736201
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135300605329152
TAF7#6879	3	6.85984164295435	0.00584328640701904	0.0262446561330866
TBP#6908	5	3.70677068709639	0.00142875510672112	0.00918602281401424
TCF7L2#6934	3	6.46210593788241	0.00693010875568919	0.0293203819459357
USF1#7391	4	5.08919942176637	0.0026686777536004	0.0147179614462836
YY1#7528	5	4.91117074985386	0.0003499314082136	0.00352731264766143

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.