Coexpression cluster:C1527

Full id: C1527_glioblastoma_Lens_mesothelioma_mesenchymal_granulosa_Ciliary_Smooth

Phase1 CAGE Peaks

Hg19::chr5:146889496..146889529,-	p2@DPYSL3
Hg19::chr5:146889532..146889549,-	p6@DPYSL3
Hg19::chr5:146889596..146889607,-	p13@DPYSL3
Hg19::chr5:146889619..146889639,-	p3@DPYSL3
Hg19::chr5:146889643..146889652,-	p11@DPYSL3
Hg19::chr5:146889655..146889679,-	p4@DPYSL3

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
non-terminally differentiated cell	2.37e-37	180
electrically responsive cell	1.18e-17	60
electrically active cell	1.18e-17	60
mesodermal cell	1.73e-17	119
smooth muscle cell	4.71e-17	42
smooth muscle myoblast	4.71e-17	42
contractile cell	6.36e-17	59
vascular associated smooth muscle cell	1.45e-16	32
muscle cell	2.19e-16	54
muscle precursor cell	1.94e-15	57
myoblast	1.94e-15	57
multi-potent skeletal muscle stem cell	1.94e-15	57
fibroblast	1.57e-14	75
embryonic cell	4.52e-14	248
neural cell	5.64e-09	25
neurectodermal cell	7.10e-09	59
cardiocyte	1.75e-07	16
glial cell (sensu Vertebrata)	4.62e-07	15
glial cell	4.62e-07	15
glioblast	4.62e-07	15
glioblast (sensu Vertebrata)	4.62e-07	15
neuron associated cell	8.18e-07	17
neuron associated cell (sensu Vertebrata)	8.18e-07	17
aortic smooth muscle cell	8.79e-07	10

Uber Anatomy

Ontology term	p-value	n
splanchnic layer of lateral plate mesoderm	1.39e-27	84
blood vessel	4.99e-25	60
epithelial tube open at both ends	4.99e-25	60
blood vasculature	4.99e-25	60
vascular cord	4.99e-25	60
vasculature	5.27e-25	79
vascular system	5.27e-25	79
epithelial tube	3.51e-23	118
cell layer	7.63e-23	312
epithelium	9.38e-23	309
artery	3.52e-22	42
arterial blood vessel	3.52e-22	42
arterial system	3.52e-22	42
vessel	1.52e-21	69
multi-cellular organism	4.14e-21	659
anatomical cluster	4.76e-21	286
anatomical conduit	3.65e-20	241
tube	5.46e-20	194
cardiovascular system	1.22e-19	110
organism subdivision	2.65e-19	365
circulatory system	3.73e-19	113
anatomical system	1.78e-18	625
anatomical group	3.77e-18	626
multi-tissue structure	5.94e-18	347
systemic artery	8.35e-18	33
systemic arterial system	8.35e-18	33
somite	2.92e-16	83
paraxial mesoderm	2.92e-16	83
presomitic mesoderm	2.92e-16	83
presumptive segmental plate	2.92e-16	83
trunk paraxial mesoderm	2.92e-16	83
presumptive paraxial mesoderm	2.92e-16	83
dermomyotome	5.09e-16	70
muscle tissue	6.48e-16	63
musculature	6.48e-16	63
musculature of body	6.48e-16	63
embryo	6.60e-16	612
trunk mesenchyme	7.94e-16	143
skeletal muscle tissue	1.69e-15	61
striated muscle tissue	1.69e-15	61
myotome	1.69e-15	61
unilaminar epithelium	1.43e-14	138
embryonic structure	1.99e-14	605
developing anatomical structure	1.99e-14	605
germ layer	4.02e-14	604
embryonic tissue	4.02e-14	604
presumptive structure	4.02e-14	604
epiblast (generic)	4.02e-14	604
multilaminar epithelium	1.86e-13	82
aorta	1.39e-11	21
aortic system	1.39e-11	21
ectoderm-derived structure	1.43e-10	169
ectoderm	5.72e-10	173
presumptive ectoderm	5.72e-10	173
trunk	2.36e-09	216
heart	4.93e-09	24
primitive heart tube	4.93e-09	24
primary heart field	4.93e-09	24
anterior lateral plate mesoderm	4.93e-09	24
heart tube	4.93e-09	24
heart primordium	4.93e-09	24
cardiac mesoderm	4.93e-09	24
cardiogenic plate	4.93e-09	24
heart rudiment	4.93e-09	24
mesenchyme	2.40e-08	238
entire embryonic mesenchyme	2.40e-08	238
primary circulatory organ	3.82e-08	27
compound organ	7.64e-08	69
organ part	9.03e-08	219
head	1.25e-07	123
smooth muscle tissue	2.94e-07	15
anterior region of body	4.65e-07	129
craniocervical region	4.65e-07	129
neural plate	7.76e-07	86

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	6	5.36025637307503	4.21437267579784e-05	0.000756002864801873
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380704118399273
RAD21#5885	6	10.3550338954563	8.10515055094479e-07	3.54329769104279e-05
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.0057369556853521
TBP#6908	6	3.70677068709639	0.00038541647290796	0.00378099859233838
ZNF263#10127	6	8.22184163701068	3.23542093046082e-06	0.000108825805654234

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.