Coexpression cluster:C3994

Full id: C3994_pituitary_ovary_putamen_pancreas_glioblastoma_Smooth_gall

Phase1 CAGE Peaks

Hg19::chr1:68516345..68516360,-	p4@DIRAS3
Hg19::chr1:68516361..68516380,-	p3@DIRAS3
Hg19::chr1:68516393..68516402,-	p6@DIRAS3

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
contractile cell	2.14e-17	59
muscle cell	2.27e-16	54
non-terminally differentiated cell	4.69e-16	180
muscle precursor cell	5.43e-16	57
myoblast	5.43e-16	57
multi-potent skeletal muscle stem cell	5.43e-16	57
electrically responsive cell	1.13e-14	60
electrically active cell	1.13e-14	60
smooth muscle cell	2.82e-13	42
smooth muscle myoblast	2.82e-13	42
vascular associated smooth muscle cell	3.19e-12	32
mesodermal cell	1.43e-11	119
fibroblast	1.07e-08	75

Uber Anatomy

Ontology term	p-value	n
anatomical cluster	2.04e-22	286
anatomical conduit	1.43e-21	241
epithelium	4.39e-20	309
tube	5.18e-20	194
cell layer	6.99e-20	312
multi-tissue structure	8.28e-19	347
adult organism	3.65e-18	115
organism subdivision	3.10e-16	365
splanchnic layer of lateral plate mesoderm	6.27e-16	84
muscle tissue	8.92e-15	63
musculature	8.92e-15	63
musculature of body	8.92e-15	63
epithelial tube	1.38e-14	118
skeletal muscle tissue	1.72e-14	61
striated muscle tissue	1.72e-14	61
myotome	1.72e-14	61
circulatory system	4.99e-14	113
vasculature	1.01e-13	79
vascular system	1.01e-13	79
anatomical group	5.63e-13	626
somite	6.05e-13	83
paraxial mesoderm	6.05e-13	83
presomitic mesoderm	6.05e-13	83
presumptive segmental plate	6.05e-13	83
trunk paraxial mesoderm	6.05e-13	83
presumptive paraxial mesoderm	6.05e-13	83
cardiovascular system	6.44e-13	110
dermomyotome	7.10e-13	70
neural plate	8.04e-13	86
presumptive neural plate	8.04e-13	86
anatomical system	8.58e-13	625
multi-cellular organism	1.81e-12	659
vessel	3.21e-12	69
trunk mesenchyme	5.20e-12	143
neurectoderm	6.57e-12	90
blood vessel	1.37e-11	60
epithelial tube open at both ends	1.37e-11	60
blood vasculature	1.37e-11	60
vascular cord	1.37e-11	60
primary circulatory organ	3.80e-11	27
multilaminar epithelium	1.40e-10	82
artery	1.64e-10	42
arterial blood vessel	1.64e-10	42
arterial system	1.64e-10	42
unilaminar epithelium	3.31e-10	138
heart	9.04e-10	24
primitive heart tube	9.04e-10	24
primary heart field	9.04e-10	24
anterior lateral plate mesoderm	9.04e-10	24
heart tube	9.04e-10	24
heart primordium	9.04e-10	24
cardiac mesoderm	9.04e-10	24
cardiogenic plate	9.04e-10	24
heart rudiment	9.04e-10	24
head	1.71e-09	123
central nervous system	1.78e-09	82
anterior region of body	2.46e-09	129
craniocervical region	2.46e-09	129
regional part of nervous system	3.14e-09	94
nervous system	3.14e-09	94
neural tube	4.47e-09	57
neural rod	4.47e-09	57
future spinal cord	4.47e-09	57
neural keel	4.47e-09	57
germ layer	1.66e-08	604
embryonic tissue	1.66e-08	604
presumptive structure	1.66e-08	604
epiblast (generic)	1.66e-08	604
embryonic structure	2.23e-08	605
developing anatomical structure	2.23e-08	605
regional part of brain	2.42e-08	59
embryo	4.44e-08	612
pre-chordal neural plate	4.60e-08	61
brain	5.20e-08	69
future brain	5.20e-08	69
compound organ	2.15e-07	69
systemic artery	2.89e-07	33
systemic arterial system	2.89e-07	33

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)
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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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No analysis results for this cluster

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.