Coexpression cluster:C2150

Full id: C2150_left_heart_tongue_diaphragm_skeletal_throat_iPS

Phase1 CAGE Peaks

Hg19::chr11:63742116..63742139,+	p1@ENST00000535431
Hg19::chr16:2009598..2009610,+	p2@NDUFB10
Hg19::chr16:58768148..58768173,-	p2@GOT2
Hg19::chr17:46970196..46970219,+	p2@ATP5G1

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
6.34702985400389e-05	0.00669611649597411	2	132	Oxidative phosphorylation (KEGG):00190
6.31961929821581e-05	0.00669611649597411	3	1138	Metabolic pathways (KEGG):01100
0.000101670189141599	0.00919388996094747	2	167	Alzheimer's disease (KEGG):05010
6.15571812123322e-05	0.00669611649597411	2	130	Parkinson's disease (KEGG):05012
0.000122103636745775	0.00966145025750944	2	183	Huntington's disease (KEGG):05016
4.32324164114602e-05	0.00669611649597411	2	109	Electron Transport Chain (Wikipathways):WP111
1.30154892898757e-05	0.00669611649597411	2	60	Oxidative phosphorylation (Wikipathways):WP623
2.38132621447758e-05	0.00669611649597411	2	81	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. (Reactome):REACT_6305

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	6.82918866373343e-05
GO:0019866	organelle inner membrane	6.82918866373343e-05
GO:0031966	mitochondrial membrane	7.60730372543529e-05
GO:0005740	mitochondrial envelope	7.60730372543529e-05
GO:0044429	mitochondrial part	0.000131288369820187
GO:0031967	organelle envelope	0.000131288369820187
GO:0031975	envelope	0.000131288369820187
GO:0005739	mitochondrion	0.00047366066166673
GO:0044455	mitochondrial membrane part	0.00062342863819871
GO:0006119	oxidative phosphorylation	0.000970045477986535
GO:0031090	organelle membrane	0.00118959530382525
GO:0004069	aspartate transaminase activity	0.00219291790159512
GO:0006533	aspartate catabolic process	0.003759066507952
GO:0006531	aspartate metabolic process	0.003759066507952
GO:0009068	aspartate family amino acid catabolic process	0.00613926641404257
GO:0005753	mitochondrial proton-transporting ATP synthase complex	0.00986522591619858
GO:0045263	proton-transporting ATP synthase complex, coupling factor F(o)	0.0124210485008482
GO:0033177	proton-transporting two-sector ATPase complex, proton-transporting domain	0.0124210485008482
GO:0044446	intracellular organelle part	0.0133772210105688
GO:0044422	organelle part	0.0133772210105688
GO:0045259	proton-transporting ATP synthase complex	0.014401696749241
GO:0006091	generation of precursor metabolites and energy	0.0151895890322062
GO:0044444	cytoplasmic part	0.0153386794966899
GO:0009066	aspartate family amino acid metabolic process	0.0153386794966899
GO:0030964	NADH dehydrogenase complex (quinone)	0.0209292682243403
GO:0045271	respiratory chain complex I	0.0209292682243403
GO:0005747	mitochondrial respiratory chain complex I	0.0209292682243403
GO:0008483	transaminase activity	0.0215879191646015
GO:0006120	mitochondrial electron transport, NADH to ubiquinone	0.0236841567176141
GO:0016310	phosphorylation	0.0236841567176141
GO:0016769	transferase activity, transferring nitrogenous groups	0.0236841567176141
GO:0050136	NADH dehydrogenase (quinone) activity	0.0236841567176141
GO:0008137	NADH dehydrogenase (ubiquinone) activity	0.0236841567176141
GO:0003954	NADH dehydrogenase activity	0.0236841567176141
GO:0046933	hydrogen ion transporting ATP synthase activity, rotational mechanism	0.0236841567176141
GO:0046961	hydrogen ion transporting ATPase activity, rotational mechanism	0.0236841567176141
GO:0042775	organelle ATP synthesis coupled electron transport	0.0236841567176141
GO:0016655	oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor	0.0236841567176141
GO:0005746	mitochondrial respiratory chain	0.0236841567176141
GO:0042773	ATP synthesis coupled electron transport	0.0236841567176141
GO:0015985	energy coupled proton transport, down electrochemical gradient	0.0236841567176141
GO:0015986	ATP synthesis coupled proton transport	0.0236841567176141
GO:0006793	phosphorus metabolic process	0.0236841567176141
GO:0006796	phosphate metabolic process	0.0236841567176141
GO:0006754	ATP biosynthetic process	0.0236841567176141
GO:0006753	nucleoside phosphate metabolic process	0.0236841567176141
GO:0009063	amino acid catabolic process	0.0242944952463599
GO:0046034	ATP metabolic process	0.024698602515066
GO:0009310	amine catabolic process	0.024698602515066
GO:0019829	cation-transporting ATPase activity	0.024698602515066
GO:0044270	nitrogen compound catabolic process	0.024698602515066
GO:0016469	proton-transporting two-sector ATPase complex	0.026727949683397
GO:0016651	oxidoreductase activity, acting on NADH or NADPH	0.026727949683397
GO:0030170	pyridoxal phosphate binding	0.0272202797454679
GO:0009145	purine nucleoside triphosphate biosynthetic process	0.0272202797454679
GO:0009206	purine ribonucleoside triphosphate biosynthetic process	0.0272202797454679
GO:0009201	ribonucleoside triphosphate biosynthetic process	0.0272202797454679
GO:0005737	cytoplasm	0.0272202797454679
GO:0009142	nucleoside triphosphate biosynthetic process	0.0272202797454679
GO:0009205	purine ribonucleoside triphosphate metabolic process	0.0272202797454679
GO:0009144	purine nucleoside triphosphate metabolic process	0.0272202797454679
GO:0009199	ribonucleoside triphosphate metabolic process	0.0272202797454679
GO:0015992	proton transport	0.0272202797454679
GO:0006818	hydrogen transport	0.0272202797454679
GO:0006869	lipid transport	0.0272202797454679
GO:0006752	group transfer coenzyme metabolic process	0.027401158131206
GO:0009141	nucleoside triphosphate metabolic process	0.0283221990602095
GO:0009152	purine ribonucleotide biosynthetic process	0.0283221990602095
GO:0009150	purine ribonucleotide metabolic process	0.0293294340550967
GO:0009260	ribonucleotide biosynthetic process	0.0293294340550967
GO:0006164	purine nucleotide biosynthetic process	0.0293294340550967
GO:0006163	purine nucleotide metabolic process	0.029991643053738
GO:0009259	ribonucleotide metabolic process	0.029991643053738
GO:0009058	biosynthetic process	0.029991643053738
GO:0031980	mitochondrial lumen	0.0315133858777004
GO:0005759	mitochondrial matrix	0.0315133858777004
GO:0009108	coenzyme biosynthetic process	0.0330769873577077
GO:0043231	intracellular membrane-bound organelle	0.0330769873577077
GO:0043227	membrane-bound organelle	0.0330769873577077
GO:0015078	hydrogen ion transmembrane transporter activity	0.0331900151934134
GO:0042625	ATPase activity, coupled to transmembrane movement of ions	0.0334222348775195
GO:0015077	monovalent inorganic cation transmembrane transporter activity	0.0346519919713304
GO:0051188	cofactor biosynthetic process	0.0346519919713304
GO:0043234	protein complex	0.0361460514474408
GO:0019842	vitamin binding	0.0376539411407996
GO:0009055	electron carrier activity	0.0382786005924434
GO:0009165	nucleotide biosynthetic process	0.0382786005924434
GO:0016020	membrane	0.0398697691353846
GO:0022890	inorganic cation transmembrane transporter activity	0.0398697691353846
GO:0042626	ATPase activity, coupled to transmembrane movement of substances	0.0398697691353846
GO:0043492	ATPase activity, coupled to movement of substances	0.0398697691353846
GO:0016820	hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	0.0402804128244258
GO:0006732	coenzyme metabolic process	0.0404037484717721
GO:0015399	primary active transmembrane transporter activity	0.0415947791500103
GO:0015405	P-P-bond-hydrolysis-driven transmembrane transporter activity	0.0415947791500103
GO:0009117	nucleotide metabolic process	0.0460605578777584
GO:0051186	cofactor metabolic process	0.0460605578777584
GO:0043229	intracellular organelle	0.0477710713261117
GO:0043226	organelle	0.0477710713261117
GO:0055086	nucleobase, nucleoside and nucleotide metabolic process	0.0477710713261117

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	3.79e-17	254
embryonic cell	2.88e-10	248

Uber Anatomy

Ontology term	p-value	n
multi-tissue structure	4.92e-20	347
cell layer	2.27e-15	312
epithelium	5.07e-15	309
mesenchyme	7.48e-14	238
entire embryonic mesenchyme	7.48e-14	238
anatomical conduit	9.76e-14	241
anatomical cluster	2.57e-13	286
tube	1.10e-12	194
organism subdivision	5.78e-12	365
compound organ	1.66e-10	69
epithelial tube	7.42e-10	118
trunk	1.10e-09	216
organ part	1.25e-08	219
trunk mesenchyme	4.89e-08	143
subdivision of trunk	2.72e-07	113
unilaminar epithelium	2.94e-07	138
primordium	4.66e-07	168
embryo	6.42e-07	612
organ segment	8.63e-07	97

Disease

Ontology term	p-value	n
carcinoma	1.30e-12	106
cell type cancer	2.12e-11	143
disease of cellular proliferation	7.40e-11	239
cancer	8.58e-11	235

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
ATF3#467	2	11.2315872630044	0.0111955903992222	0.041120318822028
CCNT2#905	3	4.75215118272197	0.0138620699668949	0.0487012051425483
E2F4#1874	4	12.6680603152844	3.88145892637771e-05	0.000725569516398715
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00995091370856955
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101279083737506
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160561003115966
ETS1#2113	4	9.72876092220234	0.000111595531741814	0.00154328995492363
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378374226260029
GTF2F1#2962	3	9.55474565756824	0.00182036231930478	0.0108961955677368
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185580422210487
IRF1#3659	3	5.72787281517293	0.00809711479033333	0.0319863292074901
IRF3#3661	2	23.4909761057448	0.00264110142537554	0.0145913029922131
IRF4#3662	2	10.9572563433721	0.0117453018068803	0.0428156221783168
JUND#3727	3	5.24599795640327	0.0104343275174842	0.038666952829668
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0465937443844233
MXI1#4601	4	9.9615716287593	0.000101522475495045	0.0014213010480197
MYC#4609	4	5.2222818716094	0.00134430939527274	0.0088568211539799
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.00766497672826024
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.0434750654889777
POU2F2#5452	4	9.10612405774252	0.00014539566517493	0.00188095848819577
RAD21#5885	3	7.76627542159225	0.003341119385872	0.0172624501603387
RFX5#5993	3	9.03593312039632	0.00214456119132407	0.0123805110972691
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00794495674036343
SP2#6668	3	19.6151478703835	0.000217100426924534	0.00248479468356946
SPI1#6688	3	6.15324263139204	0.00658038711305903	0.0280899636107567
STAT1#6772	2	10.3532937485996	0.0131077747617126	0.0464843086023261
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321294099971372
TAF7#6879	3	8.57480205369294	0.0025005543351524	0.0140270380389398
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243516796213191
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0482748446126443
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106623836618189
ZNF143#7702	3	10.1256574141709	0.00153486161068818	0.0097606656371347

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.