Coexpression cluster:C453

Full id: C453_hepatic_Ewing_neurofibroma_spindle_tridermal_Olfactory_bone

Phase1 CAGE Peaks

Hg19::chr15:33025921..33025938,+	p@chr15:33025921..33025938 +
Hg19::chr15:39882081..39882094,+	p@chr15:39882081..39882094 +
Hg19::chr15:39882095..39882106,+	p@chr15:39882095..39882106 +
Hg19::chr15:39883408..39883415,+	p37@THBS1
Hg19::chr15:39888563..39888574,+	p@chr15:39888563..39888574 +
Hg19::chr15:39888595..39888609,+	p@chr15:39888595..39888609 +
Hg19::chr15:39888702..39888705,+	p@chr15:39888702..39888705 +
Hg19::chr15:39888716..39888727,+	p@chr15:39888716..39888727 +
Hg19::chr15:39888784..39888798,+	p@chr15:39888784..39888798 +
Hg19::chr15:39888826..39888850,+	p@chr15:39888826..39888850 +
Hg19::chr15:39888934..39888945,+	p@chr15:39888934..39888945 +
Hg19::chr15:39889064..39889095,+	p@chr15:39889064..39889095 +
Hg19::chr15:39889119..39889166,+	p@chr15:39889119..39889166 +
Hg19::chr15:39889167..39889181,+	p@chr15:39889167..39889181 +
Hg19::chr15:39889186..39889187,+	p@chr15:39889186..39889187 +
Hg19::chr15:39889193..39889209,+	p@chr15:39889193..39889209 +
Hg19::chr15:39889224..39889239,+	p@chr15:39889224..39889239 +
Hg19::chr15:39889243..39889260,+	p@chr15:39889243..39889260 +
Hg19::chr15:39889273..39889278,+	p@chr15:39889273..39889278 +
Hg19::chr15:39889279..39889395,+	p2@BC015134
Hg19::chr15:39889397..39889411,+	p4@BC015134
Hg19::chr15:39889413..39889446,+	p3@BC015134

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:0008201	heparin binding	0.0154244672082892
GO:0007596	blood coagulation	0.0154244672082892
GO:0050817	coagulation	0.0154244672082892
GO:0007599	hemostasis	0.0154244672082892
GO:0005539	glycosaminoglycan binding	0.0154244672082892
GO:0030247	polysaccharide binding	0.0154244672082892
GO:0050878	regulation of body fluid levels	0.0154244672082892
GO:0001871	pattern binding	0.0154244672082892
GO:0042060	wound healing	0.0154244672082892
GO:0004866	endopeptidase inhibitor activity	0.0256253813300793
GO:0030414	protease inhibitor activity	0.0256253813300793
GO:0051674	localization of cell	0.0298834334157541
GO:0006928	cell motility	0.0298834334157541
GO:0004857	enzyme inhibitor activity	0.0298834334157541
GO:0009611	response to wounding	0.0298834334157541
GO:0030246	carbohydrate binding	0.0316584245849523
GO:0009605	response to external stimulus	0.039458100442579
GO:0007399	nervous system development	0.042152360767691
GO:0065008	regulation of biological quality	0.0484432557904829
GO:0022610	biological adhesion	0.0484432557904829
GO:0007155	cell adhesion	0.0484432557904829

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
endothelial cell of vascular tree	2.52e-14	24
fibroblast	4.47e-14	76
mesodermal cell	3.89e-11	121
blood vessel endothelial cell	6.47e-11	18
embryonic blood vessel endothelial progenitor cell	6.47e-11	18
somatic cell	6.47e-11	588
endothelial cell	2.77e-10	36
meso-epithelial cell	6.51e-09	45
animal cell	1.44e-08	679
eukaryotic cell	1.44e-08	679
endothelial cell of artery	2.17e-07	9
preadipocyte	4.17e-07	12
lining cell	5.66e-07	58
barrier cell	5.66e-07	58
skin fibroblast	8.78e-07	23
embryonic cell	9.95e-07	250

Uber Anatomy

Ontology term	p-value	n
vessel	1.40e-16	68
splanchnic layer of lateral plate mesoderm	9.17e-16	83
epithelial tube open at both ends	3.82e-15	59
blood vessel	3.82e-15	59
blood vasculature	3.82e-15	59
vascular cord	3.82e-15	59
vasculature	8.32e-15	78
vascular system	8.32e-15	78
artery	2.12e-12	42
arterial blood vessel	2.12e-12	42
arterial system	2.12e-12	42
epithelial tube	2.91e-11	117
simple squamous epithelium	3.72e-11	22
blood vessel endothelium	6.47e-11	18
endothelium	6.47e-11	18
cardiovascular system endothelium	6.47e-11	18
circulatory system	2.88e-10	112
cardiovascular system	3.62e-10	109
squamous epithelium	1.12e-09	25
systemic artery	4.60e-09	33
systemic arterial system	4.60e-09	33
aorta	1.24e-08	21
aortic system	1.24e-08	21
organ component layer	1.52e-08	66
mesoderm	5.03e-08	315
mesoderm-derived structure	5.03e-08	315
presumptive mesoderm	5.03e-08	315
anatomical system	5.05e-08	624
unilaminar epithelium	6.02e-08	148
anatomical group	6.62e-08	625
multi-cellular organism	1.42e-07	656
endothelial tube	2.17e-07	9
arterial system endothelium	2.17e-07	9
endothelium of artery	2.17e-07	9
lateral plate mesoderm	3.34e-07	203

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
ESR1#2099	8	11.1885830167834	2.63298906687883e-07	1.35728896917946e-05
GATA3#2625	12	14.8562816493851	2.7254465311872e-12	3.64926808039308e-10
POLR2A#5430	21	2.0498416685327	1.30673372631837e-06	5.18715179182685e-05

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.