Coexpression cluster:C1515

Full id: C1515_Endothelial_schwannoma_Renal_cerebellum_lung_heart_diaphragm

Phase1 CAGE Peaks

Hg19::chr3:34262215..34262222,+	p@chr3:34262215..34262222 +
Hg19::chr6:76203218..76203267,-	p2@FILIP1
Hg19::chr8:16424975..16425011,-	p3@MSR1
Hg19::chr8:16425014..16425019,-	p13@MSR1
Hg19::chr8:16425043..16425061,-	p5@MSR1
Hg19::chr8:16425067..16425095,-	p7@MSR1

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:0006898	receptor-mediated endocytosis	0.0301424702696338
GO:0005044	scavenger receptor activity	0.0301424702696338
GO:0005319	lipid transporter activity	0.0301424702696338
GO:0006817	phosphate transport	0.0309274304329055
GO:0010324	membrane invagination	0.0309274304329055
GO:0006897	endocytosis	0.0309274304329055
GO:0015698	inorganic anion transport	0.033439302955375
GO:0016044	membrane organization and biogenesis	0.033439302955375
GO:0006820	anion transport	0.0338056176982351

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	8.69e-24	24
endothelial cell	1.36e-19	35
blood vessel endothelial cell	1.38e-17	18
embryonic blood vessel endothelial progenitor cell	1.38e-17	18
meso-epithelial cell	2.92e-14	44
endothelial cell of artery	1.31e-09	9
lining cell	2.13e-08	57
barrier cell	2.13e-08	57
lymphangioblast	8.86e-08	6
endothelial cell of lymphatic vessel	8.86e-08	6
vascular lymphangioblast	8.86e-08	6
aortic endothelial cell	8.28e-07	6

Uber Anatomy

Ontology term	p-value	n
adult organism	1.81e-28	115
anatomical conduit	1.23e-20	241
anatomical cluster	1.85e-19	286
tube	5.17e-18	194
endothelium	1.38e-17	18
blood vessel endothelium	1.38e-17	18
cardiovascular system endothelium	1.38e-17	18
vessel	1.40e-15	69
vasculature	3.14e-15	79
vascular system	3.14e-15	79
epithelial tube	6.06e-14	118
simple squamous epithelium	4.99e-13	22
circulatory system	5.71e-13	113
splanchnic layer of lateral plate mesoderm	8.92e-13	84
blood vessel	1.59e-12	60
epithelial tube open at both ends	1.59e-12	60
blood vasculature	1.59e-12	60
vascular cord	1.59e-12	60
epithelium	3.25e-12	309
cell layer	8.95e-12	312
cardiovascular system	1.15e-11	110
squamous epithelium	1.28e-10	25
compound organ	2.84e-10	69
endothelial tube	1.31e-09	9
arterial system endothelium	1.31e-09	9
endothelium of artery	1.31e-09	9
multi-cellular organism	8.00e-08	659
anatomical system	8.45e-08	625
anatomical group	1.05e-07	626
multi-tissue structure	1.63e-07	347

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)
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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
FOS#2353	5	7.49829609074534	9.22669120642035e-05	0.00134359509607827
JUN#3725	5	10.4273576602803	1.82465747415735e-05	0.000415537291634364

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.