Coexpression cluster:C773

Full id: C773_Smooth_mesenchymal_Hair_Lymphatic_Preadipocyte_Aortic_anaplastic

Phase1 CAGE Peaks

Hg19::chr4:74735102..74735117,+	p1@CXCL1
Hg19::chr4:74735383..74735394,+	p@chr4:74735383..74735394 +
Hg19::chr4:74735431..74735449,+	p@chr4:74735431..74735449 +
Hg19::chr4:74735641..74735656,+	p@chr4:74735641..74735656 +
Hg19::chr4:74736251..74736276,+	p@chr4:74736251..74736276 +
Hg19::chr4:74736294..74736305,+	p@chr4:74736294..74736305 +
Hg19::chr4:74736340..74736359,+	p@chr4:74736340..74736359 +
Hg19::chr4:74736382..74736398,+	p@chr4:74736382..74736398 +
Hg19::chr4:74736459..74736475,+	p@chr4:74736459..74736475 +
Hg19::chr4:74736642..74736654,+	p@chr4:74736642..74736654 +
Hg19::chr4:74810127..74810130,-	p1@ENST00000502804

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:0008009	chemokine activity	0.0322890344084268
GO:0042379	chemokine receptor binding	0.0322890344084268
GO:0001664	G-protein-coupled receptor binding	0.0322890344084268
GO:0042330	taxis	0.0322890344084268
GO:0006935	chemotaxis	0.0322890344084268
GO:0007626	locomotory behavior	0.0322890344084268
GO:0008285	negative regulation of cell proliferation	0.0322890344084268
GO:0030036	actin cytoskeleton organization and biogenesis	0.0322890344084268
GO:0008083	growth factor activity	0.0322890344084268
GO:0030029	actin filament-based process	0.0322890344084268
GO:0006954	inflammatory response	0.0322890344084268
GO:0007610	behavior	0.0322890344084268
GO:0005125	cytokine activity	0.0322890344084268
GO:0009611	response to wounding	0.0396907747556811
GO:0008047	enzyme activator activity	0.0396907747556811
GO:0042127	regulation of cell proliferation	0.0396907747556811
GO:0005615	extracellular space	0.0419757447309549
GO:0006952	defense response	0.0419757447309549
GO:0042221	response to chemical stimulus	0.0419757447309549
GO:0009605	response to external stimulus	0.0428558813140233
GO:0007010	cytoskeleton organization and biogenesis	0.043859649122807
GO:0007399	nervous system development	0.043859649122807
GO:0008283	cell proliferation	0.043859649122807

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
vascular associated smooth muscle cell	1.59e-23	32
smooth muscle cell	1.18e-18	43
smooth muscle myoblast	1.18e-18	43
muscle precursor cell	3.99e-18	58
myoblast	3.99e-18	58
multi-potent skeletal muscle stem cell	3.99e-18	58
muscle cell	2.98e-16	55
contractile cell	2.16e-14	59
electrically responsive cell	1.47e-13	61
electrically active cell	1.47e-13	61
mesodermal cell	8.89e-13	121
embryonic cell	1.60e-11	250
aortic smooth muscle cell	1.16e-10	10
somatic cell	2.76e-10	588
animal cell	1.10e-09	679
eukaryotic cell	1.10e-09	679
non-terminally differentiated cell	4.41e-09	106
somatic stem cell	3.09e-08	433
multi fate stem cell	4.64e-08	427
smooth muscle cell of the subclavian artery	7.48e-08	5
stem cell	1.42e-07	441
native cell	2.79e-07	722

Uber Anatomy

Ontology term	p-value	n
artery	3.37e-29	42
arterial blood vessel	3.37e-29	42
arterial system	3.37e-29	42
systemic artery	2.47e-23	33
systemic arterial system	2.47e-23	33
vasculature	1.64e-22	78
vascular system	1.64e-22	78
vessel	3.36e-21	68
splanchnic layer of lateral plate mesoderm	4.21e-21	83
epithelial tube open at both ends	1.92e-20	59
blood vessel	1.92e-20	59
blood vasculature	1.92e-20	59
vascular cord	1.92e-20	59
cardiovascular system	5.26e-20	109
circulatory system	5.66e-19	112
multilaminar epithelium	3.50e-17	83
skeletal muscle tissue	3.66e-16	62
striated muscle tissue	3.66e-16	62
myotome	3.66e-16	62
muscle tissue	2.78e-15	64
musculature	2.78e-15	64
musculature of body	2.78e-15	64
somite	1.14e-14	71
presomitic mesoderm	1.14e-14	71
presumptive segmental plate	1.14e-14	71
dermomyotome	1.14e-14	71
trunk paraxial mesoderm	1.14e-14	71
paraxial mesoderm	2.70e-14	72
presumptive paraxial mesoderm	2.70e-14	72
mesoderm	3.99e-14	315
mesoderm-derived structure	3.99e-14	315
presumptive mesoderm	3.99e-14	315
dense mesenchyme tissue	6.25e-14	73
epithelial vesicle	4.19e-13	78
musculoskeletal system	6.95e-13	167
lateral plate mesoderm	2.44e-12	203
epithelial tube	3.80e-12	117
unilaminar epithelium	7.52e-11	148
blood vessel smooth muscle	1.16e-10	10
arterial system smooth muscle	1.16e-10	10
artery smooth muscle tissue	1.16e-10	10
aorta smooth muscle tissue	1.16e-10	10
aorta	2.84e-10	21
aortic system	2.84e-10	21
smooth muscle tissue	1.18e-08	15
developing anatomical structure	4.91e-08	581
embryonic structure	5.47e-08	564
trunk mesenchyme	5.57e-08	122
thoracic segment blood vessel	7.48e-08	5
subclavian artery	7.48e-08	5
embryo	3.30e-07	592
germ layer	4.60e-07	560
germ layer / neural crest	4.60e-07	560
embryonic tissue	4.60e-07	560
presumptive structure	4.60e-07	560
germ layer / neural crest derived structure	4.60e-07	560
epiblast (generic)	4.60e-07	560
anatomical system	7.08e-07	624
anatomical group	8.34e-07	625

Disease

Ontology term	p-value	n
female reproductive organ cancer	1.15e-07	27
ovarian cancer	3.00e-07	14
reproductive organ cancer	7.83e-07	29

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
CEBPB#1051	5	3.62324892082946	0.007443984749437	0.0307095245396765
POLR2A#5430	10	1.95223016050734	0.0030407318184143	0.0161359174017261
STAT3#6774	5	4.78157499870647	0.00219206266137762	0.0126365751665076

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.