Coexpression cluster:C1353

Full id: C1353_Mesenchymal_Preadipocyte_basal_Adipocyte_Fibroblast_Smooth_leiomyoma

Phase1 CAGE Peaks

Hg19::chr11:844406..844448,+	p4@TSPAN4
Hg19::chr19:42463447..42463513,-	p1@RABAC1
Hg19::chr20:35169885..35169911,+	p2@MYL9
Hg19::chr22:31503490..31503584,-	p1@SELM
Hg19::chr22:43045336..43045416,-	p1@CYB5R3
Hg19::chr22:43045417..43045424,-	p6@CYB5R3

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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No GOStat results

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
non-terminally differentiated cell	5.58e-35	180
mesodermal cell	2.82e-22	119
contractile cell	9.45e-22	59
muscle precursor cell	7.10e-21	57
myoblast	7.10e-21	57
multi-potent skeletal muscle stem cell	7.10e-21	57
muscle cell	6.67e-20	54
smooth muscle cell	7.80e-20	42
smooth muscle myoblast	7.80e-20	42
fibroblast	4.68e-18	75
electrically responsive cell	3.05e-17	60
electrically active cell	3.05e-17	60
vascular associated smooth muscle cell	2.50e-16	32
embryonic cell	2.54e-12	248
fat cell	1.98e-08	15
preadipocyte	5.81e-07	12

Uber Anatomy

Ontology term	p-value	n
trunk mesenchyme	7.50e-24	143
somite	2.08e-23	83
paraxial mesoderm	2.08e-23	83
presomitic mesoderm	2.08e-23	83
presumptive segmental plate	2.08e-23	83
trunk paraxial mesoderm	2.08e-23	83
presumptive paraxial mesoderm	2.08e-23	83
dermomyotome	1.72e-21	70
vasculature	2.04e-20	79
vascular system	2.04e-20	79
splanchnic layer of lateral plate mesoderm	2.29e-20	84
muscle tissue	2.44e-20	63
musculature	2.44e-20	63
musculature of body	2.44e-20	63
multilaminar epithelium	3.31e-20	82
skeletal muscle tissue	3.45e-20	61
striated muscle tissue	3.45e-20	61
myotome	3.45e-20	61
trunk	3.52e-20	216
organism subdivision	2.47e-19	365
epithelial tube	2.45e-18	118
vessel	1.06e-17	69
circulatory system	1.99e-17	113
cardiovascular system	4.91e-17	110
blood vessel	4.92e-17	60
epithelial tube open at both ends	4.92e-17	60
blood vasculature	4.92e-17	60
vascular cord	4.92e-17	60
multi-tissue structure	2.01e-16	347
artery	6.41e-16	42
arterial blood vessel	6.41e-16	42
arterial system	6.41e-16	42
unilaminar epithelium	2.50e-15	138
cell layer	8.30e-15	312
epithelium	2.09e-14	309
multi-cellular organism	2.51e-14	659
mesenchyme	4.04e-14	238
entire embryonic mesenchyme	4.04e-14	238
systemic artery	4.72e-13	33
systemic arterial system	4.72e-13	33
anatomical cluster	4.78e-13	286
anatomical system	3.24e-11	625
anatomical group	4.02e-11	626
anatomical conduit	4.31e-11	241
mesoderm	2.81e-08	448
mesoderm-derived structure	2.81e-08	448
presumptive mesoderm	2.81e-08	448
tube	3.02e-08	194
surface structure	3.18e-08	95
compound organ	6.23e-08	69
primary circulatory organ	2.28e-07	27
embryo	2.84e-07	612
aorta	3.01e-07	21
aortic system	3.01e-07	21
embryonic structure	4.21e-07	605
developing anatomical structure	4.21e-07	605
heart	4.21e-07	24
primitive heart tube	4.21e-07	24
primary heart field	4.21e-07	24
anterior lateral plate mesoderm	4.21e-07	24
heart tube	4.21e-07	24
heart primordium	4.21e-07	24
cardiac mesoderm	4.21e-07	24
cardiogenic plate	4.21e-07	24
heart rudiment	4.21e-07	24
smooth muscle tissue	4.51e-07	15
germ layer	5.73e-07	604
embryonic tissue	5.73e-07	604
presumptive structure	5.73e-07	604
epiblast (generic)	5.73e-07	604

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
CTBP2#1488	2	20.905666779776	0.00365309513216369	0.018450798070802
CTCF#10664	5	4.46688031089586	0.00114484834617236	0.00783479565073684
EGR1#1958	5	4.15681591234178	0.00161796681886444	0.0101300183799163
ELF1#1997	5	3.54841496567295	0.00344683777572169	0.0175243058348066
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380011212720019
SMC3#9126	3	7.52246642246642	0.00503954071682855	0.0234809097891973
TAF1#6872	5	2.78587190478774	0.0107863634029041	0.0397865722764674

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.