Coexpression cluster:C2724

Full id: C2724_Hep2_epitheloid_giant_Lymphatic_large_clear_Mesothelial

Phase1 CAGE Peaks

Hg19::chr3:149087248..149087262,-	p3@TM4SF1
Hg19::chr3:149087622..149087670,-	p@chr3:149087622..149087670 -
Hg19::chr3:149089491..149089519,-	p1@AK023364
Hg19::chr3:149095424..149095445,-	p1@TM4SF1

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
mesodermal cell	6.73e-25	119
epithelial cell	9.47e-19	254
embryonic cell	2.06e-16	248
lining cell	2.36e-15	57
barrier cell	2.36e-15	57
endothelial cell of vascular tree	6.36e-13	24
meso-epithelial cell	2.22e-12	44
squamous epithelial cell	7.86e-12	62
endothelial cell	5.28e-11	35
contractile cell	3.72e-10	59
muscle cell	4.92e-10	54
vascular associated smooth muscle cell	7.98e-10	32
muscle precursor cell	8.57e-10	57
myoblast	8.57e-10	57
multi-potent skeletal muscle stem cell	8.57e-10	57
blood vessel endothelial cell	2.02e-09	18
embryonic blood vessel endothelial progenitor cell	2.02e-09	18
smooth muscle cell	2.38e-09	42
smooth muscle myoblast	2.38e-09	42
non-terminally differentiated cell	3.20e-08	180
electrically responsive cell	2.56e-07	60
electrically active cell	2.56e-07	60

Uber Anatomy

Ontology term	p-value	n
anatomical cluster	2.85e-31	286
epithelial tube	6.60e-29	118
cell layer	3.49e-25	312
multi-tissue structure	5.10e-25	347
anatomical conduit	5.21e-25	241
epithelium	1.55e-24	309
mesenchyme	4.78e-24	238
entire embryonic mesenchyme	4.78e-24	238
vasculature	3.49e-23	79
vascular system	3.49e-23	79
vessel	2.10e-22	69
splanchnic layer of lateral plate mesoderm	5.61e-22	84
unilaminar epithelium	2.23e-20	138
blood vessel	2.37e-20	60
epithelial tube open at both ends	2.37e-20	60
blood vasculature	2.37e-20	60
vascular cord	2.37e-20	60
tube	1.38e-19	194
anatomical system	2.92e-18	625
trunk mesenchyme	3.42e-18	143
anatomical group	6.63e-18	626
multi-cellular organism	3.03e-17	659
trunk	2.68e-16	216
circulatory system	7.73e-16	113
cardiovascular system	1.07e-15	110
artery	5.31e-15	42
arterial blood vessel	5.31e-15	42
arterial system	5.31e-15	42
organism subdivision	6.66e-14	365
mesoderm	1.34e-13	448
mesoderm-derived structure	1.34e-13	448
presumptive mesoderm	1.34e-13	448
embryonic structure	2.44e-13	605
developing anatomical structure	2.44e-13	605
germ layer	3.03e-13	604
embryonic tissue	3.03e-13	604
presumptive structure	3.03e-13	604
epiblast (generic)	3.03e-13	604
systemic artery	1.47e-12	33
systemic arterial system	1.47e-12	33
embryo	1.66e-12	612
primordium	6.72e-11	168
simple squamous epithelium	8.79e-11	22
squamous epithelium	2.91e-10	25
somite	3.94e-10	83
paraxial mesoderm	3.94e-10	83
presomitic mesoderm	3.94e-10	83
presumptive segmental plate	3.94e-10	83
trunk paraxial mesoderm	3.94e-10	83
presumptive paraxial mesoderm	3.94e-10	83
digestive system	6.93e-10	155
digestive tract	6.93e-10	155
primitive gut	6.93e-10	155
skeletal muscle tissue	1.23e-09	61
striated muscle tissue	1.23e-09	61
myotome	1.23e-09	61
multilaminar epithelium	1.38e-09	82
muscle tissue	1.60e-09	63
musculature	1.60e-09	63
musculature of body	1.60e-09	63
endoderm-derived structure	1.88e-09	169
endoderm	1.88e-09	169
presumptive endoderm	1.88e-09	169
endothelium	2.02e-09	18
blood vessel endothelium	2.02e-09	18
cardiovascular system endothelium	2.02e-09	18
dermomyotome	2.24e-09	70
compound organ	6.62e-09	69
mixed endoderm/mesoderm-derived structure	7.97e-09	130
subdivision of digestive tract	8.38e-09	129
endodermal part of digestive tract	8.38e-09	129
aorta	2.45e-08	21
aortic system	2.45e-08	21
organ	8.01e-08	511
foregut	8.70e-08	98
larynx	1.55e-07	9

Disease

Ontology term	p-value	n

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
FOXA2#3170	2	12.3152318763326	0.00936191628546724	0.0353501274427099

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.