Coexpression cluster:C4324

Full id: C4324_Endothelial_Lymphatic_Hepatic_Smooth_Neutrophils_adipose_breast

Phase1 CAGE Peaks

Hg19::chr3:30647997..30648010,+	p4@TGFBR2
Hg19::chr3:30648011..30648061,+	p2@TGFBR2
Hg19::chr3:30648066..30648167,+	p1@TGFBR2

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 of vascular tree	1.26e-14	24
mesodermal cell	4.87e-14	119
endothelial cell	6.65e-14	35
blood vessel endothelial cell	9.65e-11	18
embryonic blood vessel endothelial progenitor cell	9.65e-11	18
muscle precursor cell	1.73e-10	57
myoblast	1.73e-10	57
multi-potent skeletal muscle stem cell	1.73e-10	57
meso-epithelial cell	6.95e-10	44
muscle cell	1.61e-09	54
contractile cell	3.08e-09	59
vascular associated smooth muscle cell	2.23e-08	32
smooth muscle cell	4.14e-07	42
smooth muscle myoblast	4.14e-07	42
fat cell	4.92e-07	15

Uber Anatomy

Ontology term	p-value	n
circulatory system	1.65e-29	113
cardiovascular system	3.41e-28	110
vasculature	2.02e-24	79
vascular system	2.02e-24	79
vessel	1.26e-23	69
splanchnic layer of lateral plate mesoderm	4.32e-22	84
blood vessel	1.65e-20	60
epithelial tube open at both ends	1.65e-20	60
blood vasculature	1.65e-20	60
vascular cord	1.65e-20	60
epithelial tube	5.58e-20	118
unilaminar epithelium	8.94e-17	138
artery	3.20e-15	42
arterial blood vessel	3.20e-15	42
arterial system	3.20e-15	42
systemic artery	2.30e-13	33
systemic arterial system	2.30e-13	33
muscle tissue	2.83e-11	63
musculature	2.83e-11	63
musculature of body	2.83e-11	63
skeletal muscle tissue	6.86e-11	61
striated muscle tissue	6.86e-11	61
myotome	6.86e-11	61
endothelium	9.65e-11	18
blood vessel endothelium	9.65e-11	18
cardiovascular system endothelium	9.65e-11	18
multilaminar epithelium	1.27e-10	82
dermomyotome	4.71e-10	70
trunk mesenchyme	6.03e-10	143
aorta	7.80e-10	21
aortic system	7.80e-10	21
somite	1.54e-09	83
paraxial mesoderm	1.54e-09	83
presomitic mesoderm	1.54e-09	83
presumptive segmental plate	1.54e-09	83
trunk paraxial mesoderm	1.54e-09	83
presumptive paraxial mesoderm	1.54e-09	83
mesoderm	2.80e-09	448
mesoderm-derived structure	2.80e-09	448
presumptive mesoderm	2.80e-09	448
trunk	3.05e-09	216
anatomical conduit	4.55e-09	241
simple squamous epithelium	1.82e-08	22
primary circulatory organ	2.00e-08	27
anatomical cluster	3.41e-08	286
squamous epithelium	4.82e-08	25
cell layer	1.48e-07	312
epithelium	2.49e-07	309
heart	2.89e-07	24
primitive heart tube	2.89e-07	24
primary heart field	2.89e-07	24
anterior lateral plate mesoderm	2.89e-07	24
heart tube	2.89e-07	24
heart primordium	2.89e-07	24
cardiac mesoderm	2.89e-07	24
cardiogenic plate	2.89e-07	24
heart rudiment	2.89e-07	24
anatomical system	6.21e-07	625
anatomical group	9.45e-07	626

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
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280530873298471
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326699515187938
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323469124007985
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321689694364654
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463911417006751
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167975492500545
FOS#2353	3	8.9979553088944	0.00137249927241713	0.0090005306738649
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00243643148761398
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00582842976140767
FOXA2#3170	3	24.6304637526652	6.68983856509345e-05	0.00107489238446122
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00437991528228287
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00435097269259446
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00392571695569796
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00123164916274485
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.000758961893126866
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00445416187603491
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157247539120993
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187106117418462
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00721909190586694
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295438938315704
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00309629635318249
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00137113832595742
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.0066652304185053
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00165671940770107
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277649909554233
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00203527000090648
SMARCC1#6599	3	43.6633593196315	1.20046018043203e-05	0.000302180912952858
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00310056295963411
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247341774302795
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00630541853313518
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00615995468806418
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00248978117447717
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00617626873552761

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.