Coexpression cluster:C421

Full id: C421_Smooth_Fibroblast_epithelioid_hepatic_Sertoli_Ewing_tenocyte

Phase1 CAGE Peaks

Hg19::chr10:74856613..74856631,-	p1@P4HA1
Hg19::chr5:121399703..121399718,-	p@chr5:121399703..121399718 -
Hg19::chr5:121400446..121400468,-	p@chr5:121400446..121400468 -
Hg19::chr5:121400825..121400873,-	p@chr5:121400825..121400873 -
Hg19::chr5:121400881..121400901,-	p@chr5:121400881..121400901 -
Hg19::chr5:121401627..121401642,-	p@chr5:121401627..121401642 -
Hg19::chr5:121401645..121401695,-	p@chr5:121401645..121401695 -
Hg19::chr5:121401698..121401726,-	p@chr5:121401698..121401726 -
Hg19::chr5:121401731..121401748,-	p@chr5:121401731..121401748 -
Hg19::chr5:121401877..121401903,-	p@chr5:121401877..121401903 -
Hg19::chr5:121402009..121402030,-	p@chr5:121402009..121402030 -
Hg19::chr5:121402258..121402287,-	p@chr5:121402258..121402287 -
Hg19::chr5:121406259..121406287,-	p@chr5:121406259..121406287 -
Hg19::chr5:121409731..121409737,-	p@chr5:121409731..121409737 -
Hg19::chr5:121409743..121409755,-	p@chr5:121409743..121409755 -
Hg19::chr5:121411148..121411162,-	p@chr5:121411148..121411162 -
Hg19::chr5:121411232..121411247,-	p@chr5:121411232..121411247 -
Hg19::chr5:121412666..121412683,-	p9@LOX
Hg19::chr5:121413171..121413182,-	p5@LOX
Hg19::chr5:121413944..121413965,-	p1@LOX
Hg19::chr5:121413974..121413986,-	p4@LOX
Hg19::chr5:121414004..121414025,-	p3@LOX
Hg19::chr5:121414045..121414063,-	p2@LOX
Hg19::chr5:121414152..121414179,-	p10@LOX

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:0031545	peptidyl-proline 4-dioxygenase activity	0.00429753038433406
GO:0048251	elastic fiber assembly	0.00429753038433406
GO:0004656	procollagen-proline 4-dioxygenase activity	0.00429753038433406
GO:0019798	procollagen-proline dioxygenase activity	0.00572961881385015
GO:0031543	peptidyl-proline dioxygenase activity	0.00572961881385015
GO:0004720	protein-lysine 6-oxidase activity	0.00572961881385015
GO:0030199	collagen fibril organization	0.00613869657258434
GO:0031418	L-ascorbic acid binding	0.01097934462629
GO:0016641	oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor	0.01097934462629
GO:0016638	oxidoreductase activity, acting on the CH-NH2 group of donors	0.0120286572408851
GO:0016491	oxidoreductase activity	0.0131707519804101
GO:0030324	lung development	0.0131707519804101
GO:0030323	respiratory tube development	0.0131707519804101
GO:0016706	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors	0.0131707519804101
GO:0030198	extracellular matrix organization and biogenesis	0.0131707519804101
GO:0005581	collagen	0.014493277316521
GO:0005788	endoplasmic reticulum lumen	0.0161644116411761
GO:0051213	dioxygenase activity	0.0171696269856064
GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	0.0171696269856064
GO:0016701	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen	0.0171696269856064
GO:0043062	extracellular structure organization and biogenesis	0.0171696269856064
GO:0035295	tube development	0.0218246679385887
GO:0005507	copper ion binding	0.0218246679385887
GO:0044420	extracellular matrix part	0.0234131593350398
GO:0001568	blood vessel development	0.027372249835033
GO:0001944	vasculature development	0.027372249835033
GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	0.0281005465565403
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	0.0321332748221334
GO:0019842	vitamin binding	0.0361773988863747
GO:0007167	enzyme linked receptor protein signaling pathway	0.0427874371191506
GO:0046914	transition metal ion binding	0.0490018528809785

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
non-terminally differentiated cell	5.77e-43	180
fibroblast	1.64e-24	75
mesodermal cell	2.18e-21	119
muscle precursor cell	3.56e-17	57
myoblast	3.56e-17	57
multi-potent skeletal muscle stem cell	3.56e-17	57
muscle cell	4.68e-16	54
contractile cell	3.36e-15	59
electrically responsive cell	2.03e-14	60
electrically active cell	2.03e-14	60
smooth muscle cell	2.90e-14	42
smooth muscle myoblast	2.90e-14	42
embryonic cell	1.30e-12	248
vascular associated smooth muscle cell	5.98e-12	32
skin fibroblast	1.09e-10	23
somatic cell	6.86e-09	591
preadipocyte	6.43e-08	12
animal cell	5.05e-07	679
eukaryotic cell	5.05e-07	679

Uber Anatomy

Ontology term	p-value	n
somite	4.18e-20	83
paraxial mesoderm	4.18e-20	83
presomitic mesoderm	4.18e-20	83
presumptive segmental plate	4.18e-20	83
trunk paraxial mesoderm	4.18e-20	83
presumptive paraxial mesoderm	4.18e-20	83
dermomyotome	4.50e-19	70
vasculature	1.28e-17	79
vascular system	1.28e-17	79
splanchnic layer of lateral plate mesoderm	1.55e-17	84
trunk mesenchyme	2.03e-17	143
skeletal muscle tissue	3.48e-17	61
striated muscle tissue	3.48e-17	61
myotome	3.48e-17	61
muscle tissue	1.04e-16	63
musculature	1.04e-16	63
musculature of body	1.04e-16	63
multilaminar epithelium	1.14e-16	82
vessel	7.26e-15	69
blood vessel	6.56e-14	60
epithelial tube open at both ends	6.56e-14	60
blood vasculature	6.56e-14	60
vascular cord	6.56e-14	60
epithelial tube	7.66e-14	118
unilaminar epithelium	1.03e-13	138
trunk	6.85e-13	216
artery	7.13e-13	42
arterial blood vessel	7.13e-13	42
arterial system	7.13e-13	42
cardiovascular system	1.04e-12	110
circulatory system	1.72e-12	113
multi-cellular organism	2.28e-12	659
systemic artery	5.81e-11	33
systemic arterial system	5.81e-11	33
organism subdivision	8.83e-11	365
mesenchyme	2.47e-09	238
entire embryonic mesenchyme	2.47e-09	238
anatomical system	2.89e-09	625
anatomical group	3.43e-09	626
multi-tissue structure	9.93e-09	347
cell layer	1.14e-08	312
epithelium	3.14e-08	309
surface structure	8.37e-08	95
anatomical cluster	1.04e-07	286
mesoderm	2.22e-07	448
mesoderm-derived structure	2.22e-07	448
presumptive mesoderm	2.22e-07	448
integument	4.26e-07	45
integumental system	4.26e-07	45
aorta	5.25e-07	21
aortic system	5.25e-07	21

Disease

Ontology term	p-value	n
ovarian cancer	2.47e-07	14

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
BHLHE40#8553	5	9.34829448895363	0.000163605887194037	0.00203511615681968

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.