Coexpression cluster:C3021

Full id: C3021_large_Fibroblast_giant_Lymphatic_medulloblastoma_Endothelial_squamous

Phase1 CAGE Peaks

Hg19::chr10:4823011..4823022,-	p@chr10:4823011..4823022 -
Hg19::chr10:4823096..4823144,-	p@chr10:4823096..4823144 -
Hg19::chr10:4823152..4823165,-	p@chr10:4823152..4823165 -

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	5.07e-31	24
mesodermal cell	5.27e-25	119
blood vessel endothelial cell	3.15e-22	18
embryonic blood vessel endothelial progenitor cell	3.15e-22	18
vascular associated smooth muscle cell	3.97e-21	32
endothelial cell	2.79e-20	35
non-terminally differentiated cell	1.22e-19	180
fibroblast	1.28e-16	75
lining cell	9.65e-16	57
barrier cell	9.65e-16	57
meso-epithelial cell	1.01e-15	44
skin fibroblast	1.04e-15	23
smooth muscle cell	1.75e-15	42
smooth muscle myoblast	1.75e-15	42
embryonic cell	3.32e-13	248
endothelial cell of artery	4.04e-13	9
muscle precursor cell	1.74e-11	57
myoblast	1.74e-11	57
multi-potent skeletal muscle stem cell	1.74e-11	57
lymphangioblast	2.03e-10	6
endothelial cell of lymphatic vessel	2.03e-10	6
vascular lymphangioblast	2.03e-10	6
muscle cell	2.27e-10	54
contractile cell	9.29e-10	59
aortic endothelial cell	1.56e-09	6
aortic smooth muscle cell	4.69e-09	10
cardiocyte	7.02e-09	16
squamous epithelial cell	7.22e-09	62
electrically responsive cell	1.23e-08	60
electrically active cell	1.23e-08	60
animal cell	1.97e-08	679
eukaryotic cell	1.97e-08	679
somatic cell	3.76e-07	591
fibroblast of tunica adventitia of artery	4.11e-07	4
fibroblast of the aortic adventitia	4.11e-07	4

Uber Anatomy

Ontology term	p-value	n
vessel	6.26e-50	69
blood vessel	1.92e-44	60
epithelial tube open at both ends	1.92e-44	60
blood vasculature	1.92e-44	60
vascular cord	1.92e-44	60
artery	3.11e-43	42
arterial blood vessel	3.11e-43	42
arterial system	3.11e-43	42
vasculature	9.19e-43	79
vascular system	9.19e-43	79
splanchnic layer of lateral plate mesoderm	1.70e-41	84
cardiovascular system	2.53e-36	110
circulatory system	8.25e-35	113
systemic artery	3.99e-33	33
systemic arterial system	3.99e-33	33
epithelial tube	3.09e-26	118
endothelium	3.15e-22	18
blood vessel endothelium	3.15e-22	18
cardiovascular system endothelium	3.15e-22	18
aorta	1.06e-20	21
aortic system	1.06e-20	21
simple squamous epithelium	2.35e-19	22
squamous epithelium	4.76e-18	25
unilaminar epithelium	2.37e-14	138
somite	1.55e-13	83
paraxial mesoderm	1.55e-13	83
presomitic mesoderm	1.55e-13	83
presumptive segmental plate	1.55e-13	83
trunk paraxial mesoderm	1.55e-13	83
presumptive paraxial mesoderm	1.55e-13	83
anatomical conduit	1.88e-13	241
endothelial tube	4.04e-13	9
arterial system endothelium	4.04e-13	9
endothelium of artery	4.04e-13	9
multilaminar epithelium	1.33e-12	82
dermomyotome	1.50e-12	70
anatomical cluster	3.07e-12	286
tube	5.78e-11	194
skeletal muscle tissue	3.19e-10	61
striated muscle tissue	3.19e-10	61
myotome	3.19e-10	61
muscle tissue	1.17e-09	63
musculature	1.17e-09	63
musculature of body	1.17e-09	63
integument	4.13e-09	45
integumental system	4.13e-09	45
blood vessel smooth muscle	4.69e-09	10
arterial system smooth muscle	4.69e-09	10
artery smooth muscle tissue	4.69e-09	10
aorta smooth muscle tissue	4.69e-09	10
epithelium	5.09e-09	309
skin of body	6.45e-09	40
cell layer	9.53e-09	312
heart	2.92e-08	24
primitive heart tube	2.92e-08	24
primary heart field	2.92e-08	24
anterior lateral plate mesoderm	2.92e-08	24
heart tube	2.92e-08	24
heart primordium	2.92e-08	24
cardiac mesoderm	2.92e-08	24

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
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0114871091351764
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0166766495855425
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00894548499201027
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00435834307359972
JUN#3725	3	12.5128291923363	0.000510331399272625	0.00442972913968033
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156089296377596
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00611533693022702

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.