Coexpression cluster:C495

Full id: C495_mesothelioma_Preadipocyte_Smooth_Multipotent_Placental_Sertoli_Adipocyte

Phase1 CAGE Peaks

Hg19::chr11:29181712..29181720,+	p@chr11:29181712..29181720 +
Hg19::chr11:7506866..7506875,+	p8@OLFML1
Hg19::chr12:116440921..116440925,-	p@chr12:116440921..116440925 -
Hg19::chr14:72053507..72053516,+	p@chr14:72053507..72053516 +
Hg19::chr15:37242699..37242705,-	p@chr15:37242699..37242705 -
Hg19::chr15:99191698..99191705,+	p13@IGF1R
Hg19::chr17:39724493..39724502,-	p@chr17:39724493..39724502 -
Hg19::chr19:39627507..39627526,+	p@chr19:39627507..39627526 +
Hg19::chr1:64506368..64506373,-	p@chr1:64506368..64506373 -
Hg19::chr3:123512832..123512846,-	p46@MYLK
Hg19::chr3:49449521..49449532,-	p2@RHOA
Hg19::chr5:167087144..167087148,-	p1@ENST00000522956
Hg19::chr5:167088934..167088938,-	p@chr5:167088934..167088938 -
Hg19::chr5:174774305..174774318,+	p@chr5:174774305..174774318 +
Hg19::chr5:174905496..174905507,+	p3@SFXN1
Hg19::chr6:125550179..125550191,+	p20@TPD52L1
Hg19::chr8:117695642..117695657,-	p@chr8:117695642..117695657 -
Hg19::chr8:74498117..74498133,-	p@chr8:74498117..74498133 -
Hg19::chr9:97562440..97562463,+	p18@C9orf3

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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p.value	FDR	nGenes	nPathway	Name
0.000339245429383648	0.0429484713599698	2	116	Vascular smooth muscle contraction (KEGG):04270
1.16148822114083e-05	0.00245074014660715	3	200	Focal adhesion (KEGG):04510
0.000134337357082296	0.0212588867582733	2	73	Adherens junction (KEGG):04520
9.48585957389088e-07	0.000600454911027293	3	87	MicroRNAs in cardiomyocyte hypertrophy (Wikipathways):WP1544
9.65003594215768e-06	0.00245074014660715	3	188	Focal Adhesion (Wikipathways):WP306

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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GO ID	GO name	FDR corrected p-value
GO:0004687	myosin light chain kinase activity	0.0435818046170126
GO:0005010	insulin-like growth factor receptor activity	0.0435818046170126
GO:0043548	phosphoinositide 3-kinase binding	0.0435818046170126
GO:0043560	insulin receptor substrate binding	0.0435818046170126
GO:0030238	male sex determination	0.0435818046170126
GO:0042346	positive regulation of NF-kappaB import into nucleus	0.0435818046170126
GO:0048009	insulin-like growth factor receptor signaling pathway	0.0435818046170126
GO:0042993	positive regulation of transcription factor import into nucleus	0.0435818046170126
GO:0042307	positive regulation of protein import into nucleus	0.0435818046170126
GO:0046824	positive regulation of nucleocytoplasmic transport	0.0435818046170126
GO:0051222	positive regulation of protein transport	0.0435818046170126
GO:0042802	identical protein binding	0.0435818046170126
GO:0042345	regulation of NF-kappaB import into nucleus	0.0435818046170126
GO:0042348	NF-kappaB import into nucleus	0.0435818046170126
GO:0000287	magnesium ion binding	0.0465671813510537
GO:0000086	G2/M transition of mitotic cell cycle	0.0465671813510537
GO:0051262	protein tetramerization	0.0465671813510537
GO:0007530	sex determination	0.0465671813510537
GO:0042990	regulation of transcription factor import into nucleus	0.0465671813510537
GO:0042991	transcription factor import into nucleus	0.0465671813510537
GO:0043450	alkene biosynthetic process	0.0465671813510537
GO:0019370	leukotriene biosynthetic process	0.0465671813510537
GO:0042306	regulation of protein import into nucleus	0.0465671813510537
GO:0033157	regulation of intracellular protein transport	0.0465671813510537

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	1.46e-15	180
mesodermal cell	8.73e-11	119
fibroblast	5.80e-09	75
vascular associated smooth muscle cell	1.31e-08	32
smooth muscle cell	5.22e-08	42
smooth muscle myoblast	5.22e-08	42
mesothelial cell	5.37e-08	19
muscle precursor cell	4.21e-07	57
myoblast	4.21e-07	57
multi-potent skeletal muscle stem cell	4.21e-07	57
electrically responsive cell	9.00e-07	60
electrically active cell	9.00e-07	60

Uber Anatomy

Ontology term	p-value	n
splanchnic layer of lateral plate mesoderm	1.40e-11	84
multi-cellular organism	2.44e-10	659
blood vessel	2.75e-10	60
epithelial tube open at both ends	2.75e-10	60
blood vasculature	2.75e-10	60
vascular cord	2.75e-10	60
vasculature	5.09e-10	79
vascular system	5.09e-10	79
artery	6.23e-10	42
arterial blood vessel	6.23e-10	42
arterial system	6.23e-10	42
vessel	1.23e-08	69
systemic artery	4.97e-08	33
systemic arterial system	4.97e-08	33
skeletal muscle tissue	8.52e-08	61
striated muscle tissue	8.52e-08	61
myotome	8.52e-08	61
anatomical system	9.62e-08	625
muscle tissue	1.04e-07	63
musculature	1.04e-07	63
musculature of body	1.04e-07	63
anatomical group	1.10e-07	626
lateral plate mesoderm	1.32e-07	216
circulatory system	2.01e-07	113
cardiovascular system	6.03e-07	110
epithelial tube	7.86e-07	118

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.