Coexpression cluster:C1920

Full id: C1920_ovary_granulosa_chorionic_Mesenchymal_Fibroblast_tubular_leiomyoma

Phase1 CAGE Peaks

Hg19::chr3:138665921..138665932,-	p6@FOXL2
Hg19::chr3:138665937..138665968,-	p1@FOXL2
Hg19::chr3:138665969..138665993,-	p2@FOXL2
Hg19::chr3:138666070..138666100,+	p1@C3orf72
Hg19::chr3:138666102..138666138,+	p3@C3orf72

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:0018993	somatic sex determination	0.000718238549393618
GO:0019101	female somatic sex determination	0.000718238549393618
GO:0002074	extraocular skeletal muscle development	0.000718238549393618
GO:0030237	female sex determination	0.000718238549393618
GO:0042703	menstruation	0.000718238549393618
GO:0060014	granulosa cell differentiation	0.00119706424898936
GO:0048048	embryonic eye morphogenesis	0.00205211014112462
GO:0048562	embryonic organ morphogenesis	0.00448899093371011
GO:0006309	DNA fragmentation during apoptosis	0.00495926617438451
GO:0001541	ovarian follicle development	0.00495926617438451
GO:0048568	embryonic organ development	0.00495926617438451
GO:0007530	sex determination	0.00495926617438451
GO:0043028	caspase regulator activity	0.00495926617438451
GO:0006921	cell structure disassembly during apoptosis	0.00495926617438451
GO:0030262	apoptotic nuclear changes	0.00495926617438451
GO:0022601	menstrual cycle phase	0.00495926617438451
GO:0022602	menstrual cycle process	0.00495926617438451
GO:0048592	eye morphogenesis	0.00495926617438451
GO:0008585	female gonad development	0.00495926617438451
GO:0046545	development of primary female sexual characteristics	0.00495926617438451
GO:0046660	female sex differentiation	0.00495926617438451
GO:0042698	menstrual cycle	0.00523715608932846
GO:0043010	camera-type eye development	0.00523715608932846
GO:0006308	DNA catabolic process	0.00523715608932846
GO:0006997	nuclear organization and biogenesis	0.0054586129753915
GO:0001654	eye development	0.00622473409474469
GO:0022411	cellular component disassembly	0.00622473409474469
GO:0043280	positive regulation of caspase activity	0.00622473409474469
GO:0008406	gonad development	0.00622473409474469
GO:0048608	reproductive structure development	0.00622473409474469
GO:0045137	development of primary sexual characteristics	0.0064430222813251
GO:0043281	regulation of caspase activity	0.0064430222813251
GO:0048609	reproductive process in a multicellular organism	0.0064430222813251
GO:0032504	multicellular organism reproduction	0.0064430222813251
GO:0007519	skeletal muscle development	0.00687456897276748
GO:0051345	positive regulation of hydrolase activity	0.00758140691026597
GO:0007548	sex differentiation	0.00779551596293073
GO:0007423	sensory organ development	0.00779551596293073
GO:0003006	reproductive developmental process	0.00779551596293073
GO:0014706	striated muscle development	0.00779551596293073
GO:0008632	apoptotic program	0.00779551596293073
GO:0048598	embryonic morphogenesis	0.00795192679685792
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0116087393448503
GO:0007517	muscle development	0.0140382989199662
GO:0006917	induction of apoptosis	0.0166287838066131
GO:0012502	induction of programmed cell death	0.0166287838066131
GO:0045893	positive regulation of transcription, DNA-dependent	0.0170390634590188
GO:0009790	embryonic development	0.0175818811570313
GO:0043085	positive regulation of catalytic activity	0.018167210367015
GO:0043065	positive regulation of apoptosis	0.018167210367015
GO:0043068	positive regulation of programmed cell death	0.018167210367015
GO:0045941	positive regulation of transcription	0.0192681303154634
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0195821642240336
GO:0022414	reproductive process	0.0200453849694401
GO:0051336	regulation of hydrolase activity	0.0200453849694401
GO:0009887	organ morphogenesis	0.0229962342569009
GO:0031325	positive regulation of cellular metabolic process	0.0229962342569009
GO:0009893	positive regulation of metabolic process	0.0242095924838711
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0257470259655509
GO:0043285	biopolymer catabolic process	0.0271733584520586
GO:0042981	regulation of apoptosis	0.0333633390686068
GO:0043067	regulation of programmed cell death	0.0333633390686068
GO:0050790	regulation of catalytic activity	0.0344868509827888
GO:0009057	macromolecule catabolic process	0.0350702416696102
GO:0006366	transcription from RNA polymerase II promoter	0.0353594362778397
GO:0065009	regulation of a molecular function	0.0365104595941756
GO:0044248	cellular catabolic process	0.043362312422346
GO:0006915	apoptosis	0.0447360010765168
GO:0012501	programmed cell death	0.0447360010765168
GO:0043565	sequence-specific DNA binding	0.0447360010765168
GO:0016265	death	0.0452889307534309
GO:0008219	cell death	0.0452889307534309
GO:0048522	positive regulation of cellular process	0.0469314778165419
GO:0009056	catabolic process	0.0472193316594588

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
skin fibroblast	3.31e-11	23
epithelial cell	5.51e-08	254

Uber Anatomy

Ontology term	p-value	n
skin of body	2.85e-12	40
integument	1.55e-11	45
integumental system	1.55e-11	45
organ part	2.33e-10	219
organ	1.32e-09	511
surface structure	3.07e-09	95
organism subdivision	3.79e-08	365
reproductive structure	1.47e-07	59
reproductive system	1.47e-07	59
organ component layer	5.92e-07	57

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	5	6.33620157696263	9.78880505817628e-05	0.00139149722535848
CEBPB#1051	5	7.97114762582482	3.10621793420244e-05	0.000628945899244219
E2F1#1869	5	4.90738921487932	0.000351281809925646	0.00353342203089902
E2F6#1876	5	5.01715573169739	0.000314497859929779	0.0032312682728191
EGR1#1958	5	4.98817909481014	0.000323739800059071	0.00330994233757899
ELF1#1997	5	4.25809795880754	0.000714241693977684	0.0057362879327388
HEY1#23462	5	4.04011104310571	0.000928885220517799	0.00674771117379554
HMGN3#9324	5	8.17854772335059	2.73180911341838e-05	0.000582616728601801
NRF1#4899	5	12.2102794477109	3.68220991173981e-06	0.000120780879702322
SMARCB1#6598	5	18.2527157811574	4.93125075403021e-07	2.3167561740898e-05
SPI1#6688	5	8.20432350852273	2.68916109982495e-05	0.000575165464068437
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135491190210426
TBP#6908	5	3.70677068709639	0.00142875510672112	0.00919791373918802
USF1#7391	5	6.36149927720796	9.59569864925045e-05	0.00137038858365796
YY1#7528	5	4.91117074985386	0.0003499314082136	0.00352935647922937
ZBTB7A#51341	5	7.3519093078759	4.65425347594289e-05	0.000816401711074906

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.