Coexpression cluster:C892

Full id: C892_mature_Adipocyte_liver_Hepatocyte_bile_lung_gall

Phase1 CAGE Peaks

Hg19::chr12:16500526..16500542,+	p4@MGST1
Hg19::chr12:16500545..16500556,+	p3@MGST1
Hg19::chr12:16500571..16500598,+	p1@MGST1
Hg19::chr12:16500599..16500618,+	p2@MGST1
Hg19::chr12:16507184..16507203,+	p7@MGST1
Hg19::chr12:16516767..16516832,+	p@chr12:16516767..16516832 +
Hg19::chr12:16516836..16516885,+	p@chr12:16516836..16516885 +
Hg19::chr2:85581643..85581663,-	p1@RETSAT
Hg19::chr2:85581666..85581696,-	p2@RETSAT

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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No results for this coexpression

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:0031968	organelle outer membrane	0.000331905677938092
GO:0019867	outer membrane	0.000331905677938092
GO:0051786	all-trans-retinol 13,14-reductase activity	0.0016484163428706
GO:0016117	carotenoid biosynthetic process	0.00269721005288041
GO:0016114	terpenoid biosynthetic process	0.00269721005288041
GO:0016109	tetraterpenoid biosynthetic process	0.00269721005288041
GO:0016116	carotenoid metabolic process	0.00269721005288041
GO:0016108	tetraterpenoid metabolic process	0.00269721005288041
GO:0031967	organelle envelope	0.00269721005288041
GO:0031975	envelope	0.00269721005288041
GO:0042572	retinol metabolic process	0.00269721005288041
GO:0001523	retinoid metabolic process	0.0038849809155795
GO:0005640	nuclear outer membrane	0.0038849809155795
GO:0016101	diterpenoid metabolic process	0.0038849809155795
GO:0005783	endoplasmic reticulum	0.00397864652795
GO:0006721	terpenoid metabolic process	0.0043262649554988
GO:0006776	vitamin A metabolic process	0.00436255589995717
GO:0006775	fat-soluble vitamin metabolic process	0.00494393887461995
GO:0006749	glutathione metabolic process	0.00494393887461995
GO:0031090	organelle membrane	0.00800270479558612
GO:0008299	isoprenoid biosynthetic process	0.00800270479558612
GO:0046148	pigment biosynthetic process	0.00831260284832906
GO:0042440	pigment metabolic process	0.00889568357393707
GO:0004364	glutathione transferase activity	0.00889568357393707
GO:0006720	isoprenoid metabolic process	0.00889568357393707
GO:0019748	secondary metabolic process	0.0100729845916541
GO:0005741	mitochondrial outer membrane	0.0135820206985407
GO:0016627	oxidoreductase activity, acting on the CH-CH group of donors	0.0135820206985407
GO:0016765	transferase activity, transferring alkyl or aryl (other than methyl) groups	0.0135820206985407
GO:0006766	vitamin metabolic process	0.0135820206985407
GO:0006790	sulfur metabolic process	0.0135820206985407
GO:0042445	hormone metabolic process	0.0135820206985407
GO:0044453	nuclear membrane part	0.0165535516388697
GO:0050660	FAD binding	0.0165535516388697
GO:0031965	nuclear membrane	0.0212881140823036
GO:0005792	microsome	0.0222008869305807
GO:0042598	vesicular fraction	0.0225319063857361
GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	0.0229747799532204
GO:0005635	nuclear envelope	0.0245295652737168
GO:0044446	intracellular organelle part	0.0302733803357529
GO:0044422	organelle part	0.0302733803357529
GO:0006732	coenzyme metabolic process	0.0330957864467546
GO:0050662	coenzyme binding	0.0330957864467546
GO:0044444	cytoplasmic part	0.03423899830737
GO:0005743	mitochondrial inner membrane	0.03423899830737
GO:0019866	organelle inner membrane	0.0348664034193558
GO:0008610	lipid biosynthetic process	0.0348664034193558
GO:0051186	cofactor metabolic process	0.0351600446510186
GO:0031966	mitochondrial membrane	0.0409301019669531
GO:0048037	cofactor binding	0.0416234381856567
GO:0005740	mitochondrial envelope	0.0416234381856567
GO:0005789	endoplasmic reticulum membrane	0.0432632584406575
GO:0042175	nuclear envelope-endoplasmic reticulum network	0.043275309226933
GO:0044432	endoplasmic reticulum part	0.047257146654818

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	6.79e-11	15
muscle precursor cell	7.15e-10	58
myoblast	7.15e-10	58
multi-potent skeletal muscle stem cell	7.15e-10	58
muscle cell	5.28e-09	55
fibroblast	6.54e-09	76
electrically responsive cell	3.12e-08	61
electrically active cell	3.12e-08	61
contractile cell	5.00e-08	59
embryonic cell	8.21e-08	250

Uber Anatomy

Ontology term	p-value	n
trunk	8.17e-17	199
organism subdivision	5.15e-16	264
multi-tissue structure	8.39e-15	342
trunk mesenchyme	2.88e-14	122
cell layer	2.09e-13	309
epithelium	2.33e-13	306
mesenchyme	4.93e-13	160
entire embryonic mesenchyme	4.93e-13	160
unilaminar epithelium	1.22e-12	148
multi-cellular organism	1.88e-12	656
multilaminar epithelium	3.47e-11	83
endoderm-derived structure	2.29e-10	160
endoderm	2.29e-10	160
presumptive endoderm	2.29e-10	160
somite	4.84e-10	71
presomitic mesoderm	4.84e-10	71
presumptive segmental plate	4.84e-10	71
dermomyotome	4.84e-10	71
trunk paraxial mesoderm	4.84e-10	71
paraxial mesoderm	5.07e-10	72
presumptive paraxial mesoderm	5.07e-10	72
dense mesenchyme tissue	1.48e-09	73
primordium	1.61e-09	160
anatomical group	2.03e-09	625
anatomical system	2.91e-09	624
embryo	3.71e-09	592
skeletal muscle tissue	1.05e-08	62
striated muscle tissue	1.05e-08	62
myotome	1.05e-08	62
muscle tissue	1.46e-08	64
musculature	1.46e-08	64
musculature of body	1.46e-08	64
immaterial anatomical entity	1.59e-08	117
anatomical cluster	1.71e-08	373
epithelial vesicle	2.23e-08	78
digestive system	2.41e-08	145
digestive tract	2.41e-08	145
primitive gut	2.41e-08	145
embryonic structure	3.15e-08	564
germ layer	4.43e-08	560
germ layer / neural crest	4.43e-08	560
embryonic tissue	4.43e-08	560
presumptive structure	4.43e-08	560
germ layer / neural crest derived structure	4.43e-08	560
epiblast (generic)	4.43e-08	560
adipose tissue	7.91e-08	14
developing anatomical structure	1.66e-07	581
subdivision of digestive tract	1.74e-07	118
surface structure	5.95e-07	99
anatomical conduit	8.24e-07	240

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
HEY1#23462	6	2.69340736207047	0.00948764347376227	0.0357434527363198
MYC#4609	6	3.4815212477396	0.00242366981145926	0.0136558940137566
NANOG#79923	4	12.9976793248945	0.000149875487338672	0.0019312579916303
RDBP#7936	2	34.1418675533389	0.00147831619975318	0.00945635239701245
SP1#6667	6	3.7989209187606	0.00150699787113838	0.0096244940172336
SREBF1#6720	6	31.3372329603255	7.34199048148931e-09	5.69257716329816e-07
STAT1#6772	4	9.20292777653298	0.000562899503225266	0.00480338763112538
TAF7#6879	6	7.62204626994928	2.97588074999805e-05	0.000616295874775028
USF1#7391	6	4.24099951813864	0.000822001744194416	0.00625995626089548

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.