Coexpression cluster:C3708

Full id: C3708_stomach_colon_hepatoblastoma_ovary_heart_Hepatic_mesothelioma

Phase1 CAGE Peaks

Hg19::chr18:19749504..19749515,+	p5@GATA6
Hg19::chr18:19749517..19749531,+	p3@GATA6
Hg19::chr18:19749541..19749557,+	p1@GATA6

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	6.60e-11	119
smooth muscle cell	1.24e-09	42
smooth muscle myoblast	1.24e-09	42
embryonic cell	7.42e-09	248
muscle cell	9.54e-09	54
vascular associated smooth muscle cell	1.01e-08	32
epithelial cell	1.21e-08	254
contractile cell	1.28e-08	59
cardiocyte	9.68e-08	16
muscle precursor cell	1.04e-07	57
myoblast	1.04e-07	57
multi-potent skeletal muscle stem cell	1.04e-07	57
electrically responsive cell	3.20e-07	60
electrically active cell	3.20e-07	60
non-terminally differentiated cell	9.44e-07	180

Uber Anatomy

Ontology term	p-value	n
epithelial tube	5.95e-28	118
splanchnic layer of lateral plate mesoderm	2.52e-21	84
unilaminar epithelium	2.98e-19	138
circulatory system	6.07e-17	113
mesenchyme	2.02e-16	238
entire embryonic mesenchyme	2.02e-16	238
trunk	4.91e-16	216
primordium	9.92e-16	168
cardiovascular system	1.65e-15	110
blood vessel	3.75e-15	60
epithelial tube open at both ends	3.75e-15	60
blood vasculature	3.75e-15	60
vascular cord	3.75e-15	60
subdivision of digestive tract	4.91e-14	129
endodermal part of digestive tract	4.91e-14	129
vasculature	5.88e-14	79
vascular system	5.88e-14	79
primary circulatory organ	8.34e-14	27
artery	3.16e-13	42
arterial blood vessel	3.16e-13	42
arterial system	3.16e-13	42
multi-tissue structure	3.39e-13	347
immaterial anatomical entity	1.27e-12	126
vessel	2.16e-12	69
heart	5.48e-12	24
primitive heart tube	5.48e-12	24
primary heart field	5.48e-12	24
anterior lateral plate mesoderm	5.48e-12	24
heart tube	5.48e-12	24
heart primordium	5.48e-12	24
cardiac mesoderm	5.48e-12	24
cardiogenic plate	5.48e-12	24
heart rudiment	5.48e-12	24
endoderm-derived structure	9.18e-12	169
endoderm	9.18e-12	169
presumptive endoderm	9.18e-12	169
cell layer	9.60e-12	312
anatomical cluster	1.18e-11	286
digestive system	1.62e-11	155
digestive tract	1.62e-11	155
primitive gut	1.62e-11	155
subdivision of trunk	1.68e-11	113
epithelium	1.69e-11	309
anatomical conduit	3.71e-11	241
tube	8.55e-11	194
compound organ	1.02e-10	69
mesoderm	1.24e-10	448
mesoderm-derived structure	1.24e-10	448
presumptive mesoderm	1.24e-10	448
trunk mesenchyme	3.58e-10	143
systemic artery	5.66e-10	33
systemic arterial system	5.66e-10	33
body cavity or lining	1.44e-09	49
mixed endoderm/mesoderm-derived structure	1.72e-09	130
gut epithelium	4.75e-09	54
endo-epithelium	6.61e-09	82
body cavity	6.72e-09	46
multi-cellular organism	1.53e-08	659
muscle tissue	1.82e-08	63
musculature	1.82e-08	63
musculature of body	1.82e-08	63
body cavity precursor	2.10e-08	63
trunk region element	4.12e-08	107
reproductive structure	4.26e-08	59
reproductive system	4.26e-08	59
gastrointestinal system	5.76e-08	35
anatomical space	9.36e-08	104
sac	1.06e-07	26
abdominal segment of trunk	1.13e-07	61
abdomen	1.13e-07	61
epithelium of foregut-midgut junction	1.18e-07	25
anatomical boundary	1.18e-07	25
hepatobiliary system	1.18e-07	25
foregut-midgut junction	1.18e-07	25
septum transversum	1.18e-07	25
skeletal muscle tissue	1.24e-07	61
striated muscle tissue	1.24e-07	61
myotome	1.24e-07	61
epithelial sac	1.35e-07	25
digestive tract diverticulum	3.15e-07	23
foregut	3.42e-07	98
hepatic diverticulum	3.98e-07	22
liver primordium	3.98e-07	22
anatomical cavity	7.31e-07	70

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
CTBP2#1488	3	62.7170003393281	4.049570681927e-06	0.000129614806144583
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279259986759085
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325077014560694
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321920219805354
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320427877900982
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00580945614646781
FOXA2#3170	3	24.6304637526652	6.68983856509345e-05	0.00107192397959465
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00663700784792589
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00308900535037495
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140090221116275
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.010934028662836

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.