Coexpression cluster:C1203

Full id: C1203_Endothelial_placenta_choriocarcinoma_Renal_Hair_Fibroblast_Myoblast

Phase1 CAGE Peaks

Hg19::chr14:75422292..75422308,-	p1@PGF
Hg19::chr14:75469710..75469725,+	p3@EIF2B2
Hg19::chr14:75469820..75469826,+	p4@EIF2B2
Hg19::chr1:22264210..22264241,+	p@chr1:22264210..22264241 +
Hg19::chr7:150329732..150329739,-	p8@GIMAP6
Hg19::chr9:116716048..116716100,+	p@chr9:116716048..116716100 +
Hg19::chrX:26933473..26933478,+	p@chrX:26933473..26933478 +

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:0005851	eukaryotic translation initiation factor 2B complex	0.0142404022998594
GO:0014003	oligodendrocyte development	0.0142404022998594
GO:0009746	response to hexose stimulus	0.0142404022998594
GO:0009749	response to glucose stimulus	0.0142404022998594
GO:0048709	oligodendrocyte differentiation	0.0142404022998594
GO:0007267	cell-cell signaling	0.0142404022998594
GO:0009408	response to heat	0.0142404022998594
GO:0021782	glial cell development	0.0142404022998594
GO:0005525	GTP binding	0.0142404022998594
GO:0032561	guanyl ribonucleotide binding	0.0142404022998594
GO:0019001	guanyl nucleotide binding	0.0142404022998594
GO:0009743	response to carbohydrate stimulus	0.0142404022998594
GO:0001541	ovarian follicle development	0.0142404022998594
GO:0043434	response to peptide hormone stimulus	0.0142404022998594
GO:0051716	cellular response to stimulus	0.0142404022998594
GO:0022601	menstrual cycle phase	0.0142404022998594
GO:0022602	menstrual cycle process	0.0142404022998594
GO:0042552	myelination	0.0142404022998594
GO:0008585	female gonad development	0.0142404022998594
GO:0009266	response to temperature stimulus	0.0142404022998594
GO:0046545	development of primary female sexual characteristics	0.0142404022998594
GO:0010001	glial cell differentiation	0.0142404022998594
GO:0046660	female sex differentiation	0.0142404022998594
GO:0007272	ensheathment of neurons	0.0143331463710477
GO:0008366	axon ensheathment	0.0143331463710477
GO:0042698	menstrual cycle	0.0143331463710477
GO:0042063	gliogenesis	0.0150557125642903
GO:0048513	organ development	0.0151118031882626
GO:0001508	regulation of action potential	0.0155730405882961
GO:0008406	gonad development	0.0189321349448705
GO:0048608	reproductive structure development	0.0189321349448705
GO:0006446	regulation of translational initiation	0.0194320767044059
GO:0045137	development of primary sexual characteristics	0.0194320767044059
GO:0048609	reproductive process in a multicellular organism	0.0194320767044059
GO:0032504	multicellular organism reproduction	0.0194320767044059
GO:0010033	response to organic substance	0.0194320767044059
GO:0048731	system development	0.0219785942562387
GO:0008201	heparin binding	0.0219785942562387
GO:0009725	response to hormone stimulus	0.0219785942562387
GO:0007548	sex differentiation	0.0228355766681232
GO:0003006	reproductive developmental process	0.0239246494356034
GO:0048869	cellular developmental process	0.0244377192355441
GO:0030154	cell differentiation	0.0244377192355441
GO:0006413	translational initiation	0.0253594105001998
GO:0005539	glycosaminoglycan binding	0.0275420356370652
GO:0048856	anatomical structure development	0.0278034830529979
GO:0030247	polysaccharide binding	0.0278034830529979
GO:0003743	translation initiation factor activity	0.0281596910833609
GO:0001871	pattern binding	0.0290530936829223
GO:0001525	angiogenesis	0.0290530936829223
GO:0022618	protein-RNA complex assembly	0.030682397488284
GO:0048514	blood vessel morphogenesis	0.0316725005081661
GO:0007275	multicellular organismal development	0.0316725005081661
GO:0048646	anatomical structure formation	0.0318832880281242
GO:0001568	blood vessel development	0.0327591185942815
GO:0009628	response to abiotic stimulus	0.0327591185942815
GO:0001944	vasculature development	0.0327591185942815
GO:0006417	regulation of translation	0.0356663193063391
GO:0031326	regulation of cellular biosynthetic process	0.0376439794609047
GO:0008135	translation factor activity, nucleic acid binding	0.0376439794609047
GO:0009889	regulation of biosynthetic process	0.0399554155439376
GO:0008284	positive regulation of cell proliferation	0.0418738061862045
GO:0007417	central nervous system development	0.0418738061862045
GO:0022613	ribonucleoprotein complex biogenesis and assembly	0.0431349501067882
GO:0008083	growth factor activity	0.0436708477324468
GO:0022008	neurogenesis	0.0445273105530129

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	1.11e-75	24
endothelial cell	1.50e-61	36
blood vessel endothelial cell	1.03e-57	18
embryonic blood vessel endothelial progenitor cell	1.03e-57	18
meso-epithelial cell	1.11e-47	45
lining cell	6.21e-38	58
barrier cell	6.21e-38	58
endothelial cell of artery	6.55e-30	9
mesodermal cell	5.92e-29	121
aortic endothelial cell	1.28e-20	6
vein endothelial cell	2.71e-20	6
lymphangioblast	3.00e-19	6
endothelial cell of lymphatic vessel	3.00e-19	6
vascular lymphangioblast	3.00e-19	6
squamous epithelial cell	1.85e-14	63
embryonic cell	3.68e-11	250
endothelial cell of umbilical vein	1.01e-10	3
capillary endothelial cell	1.08e-10	3
thoracic aorta endothelial cell	6.05e-08	2
skeletal muscle myoblast	2.14e-07	4

Uber Anatomy

Ontology term	p-value	n
blood vessel endothelium	1.03e-57	18
endothelium	1.03e-57	18
cardiovascular system endothelium	1.03e-57	18
simple squamous epithelium	2.79e-46	22
squamous epithelium	4.13e-40	25
vessel	6.10e-31	68
endothelial tube	6.55e-30	9
arterial system endothelium	6.55e-30	9
endothelium of artery	6.55e-30	9
vasculature	5.65e-26	78
vascular system	5.65e-26	78
epithelial tube open at both ends	1.33e-21	59
blood vessel	1.33e-21	59
blood vasculature	1.33e-21	59
vascular cord	1.33e-21	59
cardiovascular system	6.92e-21	109
circulatory system	4.19e-20	112
splanchnic layer of lateral plate mesoderm	7.49e-20	83
epithelial tube	1.13e-14	117
lymphatic vessel	2.99e-14	8
lymph vasculature	2.99e-14	8
lymphatic part of lymphoid system	2.99e-14	8
vein	2.93e-13	9
venous blood vessel	2.93e-13	9
venous system	2.93e-13	9
unilaminar epithelium	8.39e-13	148
lymphoid system	3.00e-11	10
microcirculatory vessel	1.08e-10	3
endothelium of capillary	1.08e-10	3
capillary	1.08e-10	3
artery	2.75e-10	42
arterial blood vessel	2.75e-10	42
arterial system	2.75e-10	42
anatomical conduit	4.25e-09	240
tube	3.18e-08	192
segment of aorta	6.05e-08	2
thoracic aorta	6.05e-08	2
aorta	5.13e-07	21
aortic system	5.13e-07	21
epithelium	9.64e-07	306
lateral plate mesoderm	9.67e-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
CTBP2#1488	2	17.9191429540938	0.00506029706377731	0.0235660556962382
FOS#2353	5	6.42711093492458	0.000293119596542414	0.00310793071505515
IRF3#3661	2	13.4234149175685	0.0088581602305654	0.0336156897031365

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.