Coexpression cluster:C758

Full id: C758_Chondrocyte_Amniotic_Smooth_Fibroblast_Pericytes_Endothelial_Urothelial

Phase1 CAGE Peaks

Hg19::chr14:75078662..75078675,-	p6@LTBP2
Hg19::chr14:75078682..75078706,-	p5@LTBP2
Hg19::chr14:75078725..75078734,-	p15@LTBP2
Hg19::chr14:75079026..75079049,-	p8@LTBP2
Hg19::chr14:75079066..75079077,-	p13@LTBP2
Hg19::chr14:75079174..75079185,-	p22@LTBP2
Hg19::chr14:75079186..75079202,-	p11@LTBP2
Hg19::chr14:75079205..75079223,-	p7@LTBP2
Hg19::chr14:75079261..75079277,-	p9@LTBP2
Hg19::chr14:75079282..75079293,-	p21@LTBP2
Hg19::chr14:75079294..75079329,-	p2@LTBP2

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	3.78e-22	180
mesodermal cell	1.10e-21	119
embryonic cell	4.85e-17	248
fibroblast	6.54e-17	75
contractile cell	3.25e-13	59
somatic cell	2.75e-12	591
endothelial cell	5.36e-12	35
muscle precursor cell	5.55e-12	57
myoblast	5.55e-12	57
multi-potent skeletal muscle stem cell	5.55e-12	57
muscle cell	5.38e-11	54
vascular associated smooth muscle cell	6.39e-11	32
meso-epithelial cell	8.80e-11	44
endothelial cell of vascular tree	1.11e-10	24
smooth muscle cell	1.40e-10	42
smooth muscle myoblast	1.40e-10	42
lining cell	5.29e-10	57
barrier cell	5.29e-10	57
blood vessel endothelial cell	1.97e-09	18
embryonic blood vessel endothelial progenitor cell	1.97e-09	18
electrically responsive cell	1.14e-08	60
electrically active cell	1.14e-08	60
animal cell	1.12e-07	679
eukaryotic cell	1.12e-07	679
preadipocyte	2.99e-07	12

Uber Anatomy

Ontology term	p-value	n
vasculature	2.21e-27	79
vascular system	2.21e-27	79
vessel	3.58e-23	69
splanchnic layer of lateral plate mesoderm	4.08e-23	84
blood vessel	1.65e-22	60
epithelial tube open at both ends	1.65e-22	60
blood vasculature	1.65e-22	60
vascular cord	1.65e-22	60
circulatory system	1.48e-20	113
cardiovascular system	1.79e-20	110
epithelial tube	1.16e-19	118
artery	1.21e-17	42
arterial blood vessel	1.21e-17	42
arterial system	1.21e-17	42
multi-cellular organism	6.06e-17	659
cell layer	7.80e-17	312
epithelium	2.91e-16	309
anatomical system	1.49e-15	625
somite	2.40e-15	83
paraxial mesoderm	2.40e-15	83
presomitic mesoderm	2.40e-15	83
presumptive segmental plate	2.40e-15	83
trunk paraxial mesoderm	2.40e-15	83
presumptive paraxial mesoderm	2.40e-15	83
anatomical group	3.08e-15	626
multilaminar epithelium	6.88e-15	82
organism subdivision	8.46e-15	365
trunk mesenchyme	2.69e-14	143
systemic artery	1.49e-13	33
systemic arterial system	1.49e-13	33
unilaminar epithelium	5.95e-13	138
trunk	8.99e-13	216
dermomyotome	2.02e-12	70
surface structure	2.83e-12	95
anatomical cluster	8.10e-12	286
skeletal muscle tissue	2.35e-11	61
striated muscle tissue	2.35e-11	61
myotome	2.35e-11	61
anatomical conduit	3.91e-11	241
muscle tissue	3.94e-11	63
musculature	3.94e-11	63
musculature of body	3.94e-11	63
aorta	4.59e-10	21
aortic system	4.59e-10	21
endothelium	1.97e-09	18
blood vessel endothelium	1.97e-09	18
cardiovascular system endothelium	1.97e-09	18
multi-tissue structure	4.01e-09	347
embryonic structure	6.65e-09	605
developing anatomical structure	6.65e-09	605
mesoderm	7.42e-09	448
mesoderm-derived structure	7.42e-09	448
presumptive mesoderm	7.42e-09	448
germ layer	7.73e-09	604
embryonic tissue	7.73e-09	604
presumptive structure	7.73e-09	604
epiblast (generic)	7.73e-09	604
simple squamous epithelium	1.56e-08	22
embryo	1.95e-08	612
squamous epithelium	3.37e-08	25
subdivision of head	4.52e-08	48
mesenchyme	4.74e-08	238
entire embryonic mesenchyme	4.74e-08	238
integument	8.67e-08	45
integumental system	8.67e-08	45
tube	3.07e-07	194
skin of body	9.33e-07	40

Disease

Ontology term	p-value	n
ovarian cancer	1.22e-07	14

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
ATF3#467	8	16.3368542007336	2.24789214598075e-09	1.92117518685829e-07
CCNT2#905	8	4.60814660142737	4.03688108190029e-05	0.000739273756466044
CTCF#10664	8	3.89836827132729	0.000140661176059471	0.00183425053895307
CTCFL#140690	7	12.5659382284382	2.34732188916212e-07	1.23377931948769e-05
EGR1#1958	8	3.62776661440737	0.000239224744164659	0.00260471153626072
POLR2A#5430	11	2.14745317655807	0.000223198342238743	0.00248540480489093
RAD21#5885	8	7.53093374215006	9.5260786570561e-07	4.06743306976403e-05
SMC3#9126	7	9.57404817404817	1.48666828013051e-06	5.73360961996125e-05
TAF1#6872	8	2.43130638963294	0.00420424418913911	0.0200185583509392
TAF7#6879	8	8.3149595672174	4.42802301552428e-07	2.11168171560886e-05
YY1#7528	8	3.57176054534826	0.000268200586690672	0.00286494845795102
ZBTB7A#51341	8	5.34684313300065	1.31319566009782e-05	0.000320816003613932
ZNF143#7702	8	9.8188193107112	1.21663595201433e-07	7.0007846937975e-06

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.