Coexpression cluster:C3289

Full id: C3289_lung_Endothelial_Renal_Hepatic_Lymphatic_adipose_breast

Phase1 CAGE Peaks

Hg19::chr12:52306161..52306194,+	p3@ACVRL1
Hg19::chr12:52306196..52306215,+	p6@ACVRL1
Hg19::chr12:52306220..52306231,+	p9@ACVRL1

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
endothelial cell	1.70e-34	36
endothelial cell of vascular tree	1.76e-32	24
meso-epithelial cell	3.37e-25	45
blood vessel endothelial cell	6.26e-25	18
embryonic blood vessel endothelial progenitor cell	6.26e-25	18
lining cell	5.15e-17	58
barrier cell	5.15e-17	58
endothelial cell of artery	3.64e-13	9
vein endothelial cell	1.32e-09	6
aortic endothelial cell	2.88e-09	6
lymphangioblast	4.43e-09	6
endothelial cell of lymphatic vessel	4.43e-09	6
vascular lymphangioblast	4.43e-09	6
fenestrated cell	2.44e-08	5
glomerular endothelial cell	2.44e-08	5

Uber Anatomy

Ontology term	p-value	n
adult organism	9.75e-56	114
anatomical cluster	3.64e-26	373
anatomical conduit	4.27e-26	240
neural tube	1.26e-25	56
neural rod	1.26e-25	56
future spinal cord	1.26e-25	56
neural keel	1.26e-25	56
tube	4.71e-25	192
blood vessel endothelium	6.26e-25	18
endothelium	6.26e-25	18
cardiovascular system endothelium	6.26e-25	18
central nervous system	4.22e-23	81
regional part of nervous system	4.42e-23	53
regional part of brain	4.42e-23	53
brain	7.39e-22	68
future brain	7.39e-22	68
nervous system	1.35e-21	89
brain grey matter	2.94e-19	34
gray matter	2.94e-19	34
simple squamous epithelium	3.52e-19	22
telencephalon	1.21e-18	34
regional part of forebrain	2.84e-18	41
forebrain	2.84e-18	41
anterior neural tube	2.84e-18	41
future forebrain	2.84e-18	41
neural plate	5.78e-18	82
presumptive neural plate	5.78e-18	82
cerebral hemisphere	3.35e-17	32
regional part of telencephalon	3.84e-17	32
neurectoderm	1.64e-16	86
squamous epithelium	4.22e-16	25
regional part of cerebral cortex	3.40e-15	22
structure with developmental contribution from neural crest	4.06e-14	132
vessel	2.97e-13	68
neocortex	3.44e-13	20
endothelial tube	3.64e-13	9
arterial system endothelium	3.64e-13	9
endothelium of artery	3.64e-13	9
cell layer	5.78e-13	309
cerebral cortex	8.84e-13	25
pallium	8.84e-13	25
epithelium	2.30e-12	306
organ system subdivision	9.23e-12	223
pre-chordal neural plate	1.22e-11	61
ecto-epithelium	1.81e-11	104
vasculature	5.47e-11	78
vascular system	5.47e-11	78
multi-cellular organism	8.29e-11	656
lymphoid system	1.67e-10	10
anatomical system	5.06e-10	624
anatomical group	6.05e-10	625
circulatory system	8.15e-10	112
splanchnic layer of lateral plate mesoderm	6.01e-09	83
lymphatic vessel	9.31e-09	8
lymph vasculature	9.31e-09	8
lymphatic part of lymphoid system	9.31e-09	8
epithelial tube open at both ends	9.55e-09	59
blood vessel	9.55e-09	59
blood vasculature	9.55e-09	59
vascular cord	9.55e-09	59
brainstem	1.26e-08	6
posterior neural tube	1.46e-08	15
chordal neural plate	1.46e-08	15
cardiovascular system	1.96e-08	109
neural nucleus	3.17e-08	9
nucleus of brain	3.17e-08	9
ectoderm-derived structure	3.32e-08	171
ectoderm	3.32e-08	171
presumptive ectoderm	3.32e-08	171
vein	7.59e-08	9
venous blood vessel	7.59e-08	9
venous system	7.59e-08	9
embryo	8.61e-08	592
developing anatomical structure	2.44e-07	581
epithelial tube	2.81e-07	117
segmental subdivision of nervous system	3.89e-07	13
gyrus	4.65e-07	6
embryonic structure	9.29e-07	564

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
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00436211228840003
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0108888945127747
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109029390438214

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.