Coexpression cluster:C211

Full id: C211_small_Hepatocyte_liver_colon_temporal_duodenum_kidney

Phase1 CAGE Peaks

Hg19::chr10:135160870..135160906,+	p1@PRAP1
Hg19::chr10:135165944..135165963,-	p1@CU687189
Hg19::chr10:70066579..70066613,-	p4@PBLD
Hg19::chr10:74714533..74714580,-	p1@PLA2G12B
Hg19::chr10:96522413..96522424,+	p2@CYP2C19
Hg19::chr10:96522430..96522444,+	p1@CYP2C19
Hg19::chr11:118900144..118900155,-	p6@SLC37A4
Hg19::chr11:118900180..118900195,-	p3@SLC37A4
Hg19::chr11:16419067..16419077,-	p23@SOX6
Hg19::chr11:17036092..17036106,-	p7@PLEKHA7
Hg19::chr11:2924521..2924577,+	p2@SLC22A18
Hg19::chr12:56623816..56623825,+	p4@SLC39A5
Hg19::chr12:56623827..56623866,+	p1@SLC39A5
Hg19::chr14:103561012..103561038,+	p2@ENST00000559843
Hg19::chr14:24774871..24774885,-	p@chr14:24774871..24774885 -
Hg19::chr14:39703112..39703135,+	p1@MIA2
Hg19::chr14:74462922..74462955,-	p3@ENTPD5
Hg19::chr15:67356427..67356442,+	p@chr15:67356427..67356442 +
Hg19::chr16:27225918..27225945,+	p4@JMJD5
Hg19::chr16:583916..583932,+	p@chr16:583916..583932 +
Hg19::chr16:66969412..66969439,+	p3@CES2
Hg19::chr17:1898875..1898901,+	p@chr17:1898875..1898901 +
Hg19::chr19:4164527..4164546,+	p@chr19:4164527..4164546 +
Hg19::chr1:100435315..100435325,+	p8@SLC35A3
Hg19::chr1:16068987..16069031,+	p1@TMEM82
Hg19::chr1:16069036..16069054,+	p2@TMEM82
Hg19::chr1:60392452..60392499,-	p2@CYP2J2
Hg19::chr1:6511322..6511327,+	p21@ESPN
Hg19::chr1:6511328..6511341,+	p8@ESPN
Hg19::chr1:6511365..6511371,+	p12@ESPN
Hg19::chr20:43024295..43024308,-	p1@ENST00000452481 p1@uc002xlx.2
Hg19::chr20:43076886..43076893,+	p@chr20:43076886..43076893 +
Hg19::chr21:45287080..45287091,+	p9@AGPAT3
Hg19::chr21:45287096..45287111,+	p5@AGPAT3
Hg19::chr2:21255446..21255458,-	p@chr2:21255446..21255458 -
Hg19::chr2:238499280..238499287,-	p7@RAB17
Hg19::chr2:44065897..44065908,-	p1@ABCG5
Hg19::chr3:119500874..119500885,+	p5@NR1I2
Hg19::chr3:119500891..119500904,+	p2@NR1I2
Hg19::chr3:119500908..119500919,+	p3@NR1I2
Hg19::chr3:185046677..185046694,+	p3@MAP3K13
Hg19::chr3:195943398..195943417,+	p1@OSTalpha
Hg19::chr3:58523104..58523127,-	p7@ACOX2
Hg19::chr4:22694573..22694609,+	p2@GBA3
Hg19::chr4:69817286..69817319,-	p2@UGT2A3
Hg19::chr5:149020928..149020943,-	p@chr5:149020928..149020943 -
Hg19::chr5:79949935..79949949,-	p5@DHFR
Hg19::chr6:133035185..133035201,-	p1@VNN1
Hg19::chr6:168227291..168227302,+	p19@MLLT4
Hg19::chr6:41006941..41006968,-	p1@UNC5CL
Hg19::chr6:43028274..43028300,+	p3@KLC4
Hg19::chr6:86099898..86099931,-	p1@ENST00000455071 p1@uc003pkm.2
Hg19::chr7:91671935..91671949,+	p@chr7:91671935..91671949 +
Hg19::chr7:99277610..99277626,-	p1@CYP3A5
Hg19::chr8:110615669..110615692,-	p11@SYBU
Hg19::chr8:27348649..27348720,+	p1@EPHX2
Hg19::chr8:67624738..67624752,+	p10@SGK3
Hg19::chr9:104187248..104187297,-	p@chr9:104187248..104187297 -
Hg19::chr9:104187769..104187778,-	p3@ALDOB
Hg19::chr9:104187775..104187786,+	p@chr9:104187775..104187786 +
Hg19::chr9:104187850..104187863,-	p2@ALDOB
Hg19::chr9:104187899..104187908,-	p4@ALDOB
Hg19::chr9:104189912..104189930,-	p@chr9:104189912..104189930 -
Hg19::chr9:104190749..104190775,+	p@chr9:104190749..104190775 +
Hg19::chr9:104192114..104192138,-	p@chr9:104192114..104192138 -
Hg19::chr9:104193143..104193169,-	p@chr9:104193143..104193169 -
Hg19::chr9:104198042..104198062,-	p1@ALDOB
Hg19::chr9:131872789..131872800,-	p5@CRAT
Hg19::chr9:32427222..32427240,+	p@chr9:32427222..32427240 +
Hg19::chrX:38211890..38211897,+	p3@OTC

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
1.15247210510591e-06	0.000243171614177346	4	59	Arachidonic acid metabolism (KEGG):00590
7.13397324646485e-08	4.51580506501225e-05	4	30	Linoleic acid metabolism (KEGG):00591
8.57251743419267e-05	0.00678300441980495	3	64	Retinol metabolism (KEGG):00830
0.000116845126210202	0.00767359370758104	3	71	Metabolism of xenobiotics by cytochrome P450 (KEGG):00980
0.000126917500912663	0.00767359370758104	3	73	Drug metabolism - cytochrome P450 (KEGG):00982
4.59754408998177e-05	0.00485040901493076	3	52	Drug metabolism - other enzymes (KEGG):00983
1.72073339083583e-07	5.44612118199539e-05	11	1138	Metabolic pathways (KEGG):01100
0.000154530311543426	0.00815147393391574	3	78	Peroxisome (KEGG):04146
0.000998589478845497	0.0371827729476	2	35	Fluoropyrimidine Activity (Wikipathways):WP1601
0.000133348389863178	0.00767359370758104	2	13	Irinotecan Pathway (Wikipathways):WP229
0.000887631566171946	0.0351169238366776	2	33	Nuclear receptors in lipid metabolism and toxicity (Wikipathways):WP299
7.42549874428589e-05	0.00671477243590424	3	61	cytochrome P450 (Wikipathways):WP43
3.60830331719628e-05	0.00456811199957049	2	7	Arachidonate Epoxygenase / Epoxide Hydrolase (Wikipathways):WP678
0.00029087055301572	0.0141631584660731	2	19	Tamoxifen metabolism (Wikipathways):WP691
3.48380348952018e-06	0.000551311902216568	5	175	metapathway biotransformation (Wikipathways):WP702
0.000579134600002315	0.0261851572715332	4	289	Metabolism of lipids and lipoproteins (Reactome):REACT_22258
0.000692868648311646	0.0292390569587515	3	130	Biological oxidations (Reactome):REACT_13433

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:0005783	endoplasmic reticulum	0.000166232769863203
GO:0044255	cellular lipid metabolic process	0.000292195308455164
GO:0006629	lipid metabolic process	0.000767639703596833
GO:0044444	cytoplasmic part	0.000767639703596833
GO:0032787	monocarboxylic acid metabolic process	0.00101187401991179
GO:0016712	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen	0.00101187401991179
GO:0044432	endoplasmic reticulum part	0.00101187401991179
GO:0019752	carboxylic acid metabolic process	0.00101187401991179
GO:0006082	organic acid metabolic process	0.00101187401991179
GO:0006631	fatty acid metabolic process	0.00254640139128139
GO:0005737	cytoplasm	0.00548687314804639
GO:0005777	peroxisome	0.00651008947141174
GO:0042579	microbody	0.00651008947141174
GO:0050381	unspecific monooxygenase activity	0.0127585701205273
GO:0042221	response to chemical stimulus	0.0127585701205273
GO:0006091	generation of precursor metabolites and energy	0.0134364792462607
GO:0006805	xenobiotic metabolic process	0.015055976095265
GO:0009410	response to xenobiotic stimulus	0.0160201134498307
GO:0008374	O-acyltransferase activity	0.0160201134498307
GO:0005792	microsome	0.0160201134498307
GO:0042598	vesicular fraction	0.0160201134498307
GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	0.0160201134498307
GO:0031090	organelle membrane	0.0160201134498307
GO:0043651	linoleic acid metabolic process	0.0160201134498307
GO:0008391	arachidonic acid monooxygenase activity	0.0160201134498307
GO:0009348	ornithine carbamoyltransferase complex	0.0160201134498307
GO:0033791	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity	0.0160201134498307
GO:0003869	4-nitrophenylphosphatase activity	0.0160201134498307
GO:0004092	carnitine O-acetyltransferase activity	0.0160201134498307
GO:0002532	production of molecular mediator of acute inflammatory response	0.0160201134498307
GO:0008392	arachidonic acid epoxygenase activity	0.0160201134498307
GO:0004585	ornithine carbamoyltransferase activity	0.0160201134498307
GO:0002539	prostaglandin production during acute inflammatory response	0.0160201134498307
GO:0002538	production of arachidonic acid metabolites during acute inflammatory response	0.0160201134498307
GO:0005789	endoplasmic reticulum membrane	0.0200455236898233
GO:0042175	nuclear envelope-endoplasmic reticulum network	0.020781869242664
GO:0019825	oxygen binding	0.020781869242664
GO:0008202	steroid metabolic process	0.020781869242664
GO:0044262	cellular carbohydrate metabolic process	0.020781869242664
GO:0031667	response to nutrient levels	0.020781869242664
GO:0004497	monooxygenase activity	0.020781869242664
GO:0042493	response to drug	0.020781869242664
GO:0005788	endoplasmic reticulum lumen	0.020781869242664
GO:0016139	glycoside catabolic process	0.020781869242664
GO:0018675	(S)-limonene 6-monooxygenase activity	0.020781869242664
GO:0018676	(S)-limonene 7-monooxygenase activity	0.020781869242664
GO:0005462	UDP-N-acetylglucosamine transmembrane transporter activity	0.020781869242664
GO:0033767	4-hydroxyacetophenone monooxygenase activity	0.020781869242664
GO:0015788	UDP-N-acetylglucosamine transport	0.020781869242664
GO:0019113	limonene monooxygenase activity	0.020781869242664
GO:0016137	glycoside metabolic process	0.020781869242664
GO:0017159	pantetheinase activity	0.020781869242664
GO:0015293	symporter activity	0.020781869242664
GO:0009991	response to extracellular stimulus	0.0213609920965642
GO:0000267	cell fraction	0.0232283299567552
GO:0016020	membrane	0.0237885008900423
GO:0044446	intracellular organelle part	0.0245242466769064
GO:0044422	organelle part	0.0245716351347396
GO:0016413	O-acetyltransferase activity	0.0267601407488756
GO:0004146	dihydrofolate reductase activity	0.0267601407488756
GO:0008422	beta-glucosidase activity	0.0267601407488756
GO:0009056	catabolic process	0.0284975497610938
GO:0020037	heme binding	0.0284975497610938
GO:0046906	tetrapyrrole binding	0.0284975497610938
GO:0008652	amino acid biosynthetic process	0.0284975497610938
GO:0005351	sugar:hydrogen ion symporter activity	0.0319907438174286
GO:0045909	positive regulation of vasodilation	0.0319907438174286
GO:0006545	glycine biosynthetic process	0.0319907438174286
GO:0012505	endomembrane system	0.0323882090546499
GO:0051119	sugar transmembrane transporter activity	0.0336469325662541
GO:0015144	carbohydrate transmembrane transporter activity	0.0345462005428184
GO:0017110	nucleoside-diphosphatase activity	0.0357711277698788
GO:0015781	pyrimidine nucleotide-sugar transport	0.0357711277698788
GO:0010043	response to zinc ion	0.0357711277698788
GO:0006047	UDP-N-acetylglucosamine metabolic process	0.0357711277698788
GO:0005543	phospholipid binding	0.0357711277698788
GO:0006807	nitrogen compound metabolic process	0.0362188514416722
GO:0005624	membrane fraction	0.0362188514416722
GO:0008643	carbohydrate transport	0.0362188514416722
GO:0015165	pyrimidine nucleotide sugar transmembrane transporter activity	0.0362188514416722
GO:0046688	response to copper ion	0.0362188514416722
GO:0003997	acyl-CoA oxidase activity	0.0362188514416722
GO:0004301	epoxide hydrolase activity	0.0362188514416722
GO:0016406	carnitine O-acyltransferase activity	0.0362188514416722
GO:0004463	leukotriene-A4 hydrolase activity	0.0362188514416722
GO:0042301	phosphate binding	0.0362188514416722
GO:0042312	regulation of vasodilation	0.0362188514416722
GO:0016743	carboxyl- or carbamoyltransferase activity	0.0362188514416722
GO:0008385	IkappaB kinase complex	0.0362188514416722
GO:0017144	drug metabolic process	0.0362188514416722
GO:0015291	secondary active transmembrane transporter activity	0.0363783846269499
GO:0043231	intracellular membrane-bound organelle	0.0363783846269499
GO:0043227	membrane-bound organelle	0.0363783846269499
GO:0046983	protein dimerization activity	0.0371343714481092
GO:0015980	energy derivation by oxidation of organic compounds	0.0371343714481092
GO:0006118	electron transport	0.0375783309344986
GO:0009309	amine biosynthetic process	0.0375783309344986
GO:0044424	intracellular part	0.0401485454015201
GO:0030299	cholesterol absorption	0.0409602751002365
GO:0019627	urea metabolic process	0.0409602751002365
GO:0016725	oxidoreductase activity, acting on CH or CH2 groups	0.0409602751002365
GO:0000050	urea cycle	0.0409602751002365
GO:0044241	lipid digestion	0.0409602751002365
GO:0004332	fructose-bisphosphate aldolase activity	0.0409602751002365
GO:0043603	amide metabolic process	0.0409602751002365
GO:0016803	ether hydrolase activity	0.0409602751002365
GO:0015307	drug:hydrogen antiporter activity	0.0447889839759333
GO:0015904	tetracycline transport	0.0447889839759333
GO:0015520	tetracycline:hydrogen antiporter activity	0.0447889839759333
GO:0044464	cell part	0.0447961671487045
GO:0005975	carbohydrate metabolic process	0.0455601062325889
GO:0015101	organic cation transmembrane transporter activity	0.0455601062325889
GO:0050892	intestinal absorption	0.0455601062325889
GO:0003841	1-acylglycerol-3-phosphate O-acyltransferase activity	0.0455601062325889
GO:0046677	response to antibiotic	0.0455601062325889
GO:0008493	tetracycline transporter activity	0.0455601062325889
GO:0045777	positive regulation of blood pressure	0.0455601062325889
GO:0042895	antibiotic transporter activity	0.0455601062325889
GO:0031941	filamentous actin	0.0455601062325889
GO:0044271	nitrogen compound biosynthetic process	0.0455741786853529
GO:0043229	intracellular organelle	0.046614361628882
GO:0043226	organelle	0.046614361628882
GO:0000186	activation of MAPKK activity	0.0476859990628521
GO:0009070	serine family amino acid biosynthetic process	0.0476859990628521
GO:0004565	beta-galactosidase activity	0.0476859990628521
GO:0000287	magnesium ion binding	0.047781640586173
GO:0042803	protein homodimerization activity	0.0494110712844477
GO:0008015	blood circulation	0.0496129124709751
GO:0003013	circulatory system process	0.0496129124709751
GO:0051384	response to glucocorticoid stimulus	0.0496129124709751
GO:0015925	galactosidase activity	0.0496129124709751

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
metabolising cell	1.12e-23	12
endopolyploid cell	1.12e-23	12
parenchymal cell	1.12e-23	12
polyploid cell	1.12e-23	12
hepatocyte	1.12e-23	12
endodermal cell	9.78e-08	58

Uber Anatomy

Ontology term	p-value	n
liver	3.84e-26	19
digestive gland	3.84e-26	19
liver bud	3.84e-26	19
epithelium of foregut-midgut junction	1.04e-24	25
anatomical boundary	1.04e-24	25
hepatobiliary system	1.04e-24	25
foregut-midgut junction	1.04e-24	25
septum transversum	1.04e-24	25
hepatic diverticulum	1.93e-22	22
liver primordium	1.93e-22	22
digestive tract diverticulum	2.01e-21	23
epithelial sac	1.26e-19	25
abdomen element	3.18e-19	54
abdominal segment element	3.18e-19	54
sac	7.82e-19	26
abdominal segment of trunk	4.26e-17	60
abdomen	4.26e-17	60
gut epithelium	4.90e-16	54
intestine	6.91e-16	17
exocrine gland	1.25e-15	31
exocrine system	1.25e-15	31
small intestine	1.68e-15	4
endocrine gland	1.01e-13	35
subdivision of digestive tract	1.53e-12	118
digestive system	3.20e-11	145
digestive tract	3.20e-11	145
primitive gut	3.20e-11	145
gastrointestinal system	7.49e-11	25
endocrine system	1.95e-10	45
endo-epithelium	6.15e-10	82
endoderm-derived structure	6.65e-10	160
endoderm	6.65e-10	160
presumptive endoderm	6.65e-10	160
gland	1.09e-09	59
trunk region element	2.55e-09	101
epididymis	4.87e-09	1
subdivision of trunk	3.34e-08	112

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	13.8240089753179	0.0093777714259441	0.0353895237562485
FOXA1#3169	17	2.69120193913647	0.000127401571527303	0.00169477680916317
FOXA2#3170	14	4.92609275053305	7.37113804995693e-07	3.27032407306479e-05
HDAC2#3066	14	2.68312404732525	0.000580923925217827	0.00487396479963244
HEY1#23462	39	2.25091900973032	3.14827382705494e-08	2.12267637329755e-06
HNF4A#3172	26	8.5919935633828	5.65805065981129e-18	1.24666909886082e-15
HNF4G#3174	27	11.0906058316295	1.6553354100915e-21	4.47879727706078e-19
RXRA#6256	13	3.72814318298189	3.77401043834215e-05	0.0007230854451844

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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