Coexpression cluster:C895

Full id: C895_Mesenchymal_Renal_Alveolar_Fibroblast_Pericytes_Trabecular_Osteoblast

Phase1 CAGE Peaks

Hg19::chr12:53693466..53693537,+	p1@C12orf10
Hg19::chr16:2933231..2933309,+	p1@FLYWCH2
Hg19::chr17:42092313..42092389,-	p1@TMEM101
Hg19::chr19:17530838..17530885,+	p1@FAM125A
Hg19::chr19:17530888..17530938,+	p2@FAM125A
Hg19::chr19:49314305..49314316,-	p2@BCAT2
Hg19::chr19:7985198..7985257,+	p1@SNAPC2
Hg19::chr3:49055991..49056026,-	p1@DALRD3
Hg19::chr9:131133622..131133661,+	p1@URM1

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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GO ID	GO name	FDR corrected p-value
GO:0009098	leucine biosynthetic process	0.00653479335923701
GO:0006549	isoleucine metabolic process	0.00653479335923701
GO:0006550	isoleucine catabolic process	0.00653479335923701
GO:0009082	branched chain family amino acid biosynthetic process	0.00980074736638496
GO:0006551	leucine metabolic process	0.00980074736638496
GO:0009301	snRNA transcription	0.00980074736638496
GO:0006420	arginyl-tRNA aminoacylation	0.0130647783764645
GO:0004814	arginine-tRNA ligase activity	0.0130647783764645
GO:0004084	branched-chain-amino-acid transaminase activity	0.0130647783764645
GO:0009083	branched chain family amino acid catabolic process	0.017633557274085
GO:0006520	amino acid metabolic process	0.0261103347061558
GO:0009081	branched chain family amino acid metabolic process	0.0261103347061558
GO:0007595	lactation	0.0295901655496141
GO:0006519	amino acid and derivative metabolic process	0.0295901655496141
GO:0006383	transcription from RNA polymerase III promoter	0.0346414888684331
GO:0009308	amine metabolic process	0.0346414888684331
GO:0006807	nitrogen compound metabolic process	0.036932758980158
GO:0019752	carboxylic acid metabolic process	0.0449410093543494
GO:0006082	organic acid metabolic process	0.0449410093543494
GO:0008483	transaminase activity	0.0449410093543494

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	1.47e-28	180
embryonic cell	9.53e-22	248
mesodermal cell	5.31e-19	119
contractile cell	3.39e-17	59
electrically responsive cell	6.53e-15	60
electrically active cell	6.53e-15	60
animal cell	9.73e-15	679
eukaryotic cell	9.73e-15	679
muscle cell	2.01e-14	54
muscle precursor cell	4.60e-14	57
myoblast	4.60e-14	57
multi-potent skeletal muscle stem cell	4.60e-14	57
somatic cell	5.23e-13	591
smooth muscle cell	7.29e-12	42
smooth muscle myoblast	7.29e-12	42
epithelial cell	3.53e-10	254
fibroblast	3.23e-09	75
vascular associated smooth muscle cell	9.11e-09	32
meso-epithelial cell	3.22e-08	44
epithelial cell of nephron	4.82e-08	16
kidney cell	9.81e-08	18
kidney epithelial cell	9.81e-08	18
native cell	1.08e-07	722
endothelial cell	1.25e-07	35
ectodermal cell	3.37e-07	71
kidney cortical cell	8.64e-07	13
renal cortical epithelial cell	8.64e-07	13

Uber Anatomy

Ontology term	p-value	n
multilaminar epithelium	5.05e-15	82
dermomyotome	5.96e-15	70
somite	8.37e-15	83
paraxial mesoderm	8.37e-15	83
presomitic mesoderm	8.37e-15	83
presumptive segmental plate	8.37e-15	83
trunk paraxial mesoderm	8.37e-15	83
presumptive paraxial mesoderm	8.37e-15	83
vasculature	7.23e-14	79
vascular system	7.23e-14	79
mesenchyme	3.77e-13	238
entire embryonic mesenchyme	3.77e-13	238
trunk	7.16e-13	216
trunk mesenchyme	9.34e-13	143
skeletal muscle tissue	2.11e-12	61
striated muscle tissue	2.11e-12	61
myotome	2.11e-12	61
unilaminar epithelium	3.47e-12	138
splanchnic layer of lateral plate mesoderm	9.62e-12	84
epithelial tube	1.35e-11	118
muscle tissue	1.81e-11	63
musculature	1.81e-11	63
musculature of body	1.81e-11	63
vessel	3.06e-11	69
multi-tissue structure	1.14e-10	347
blood vessel	3.24e-10	60
epithelial tube open at both ends	3.24e-10	60
blood vasculature	3.24e-10	60
vascular cord	3.24e-10	60
artery	7.43e-10	42
arterial blood vessel	7.43e-10	42
arterial system	7.43e-10	42
organism subdivision	2.00e-09	365
cell layer	2.27e-09	312
epithelium	5.92e-09	309
cardiovascular system	1.01e-08	110
nephron epithelium	4.82e-08	16
nephron	4.82e-08	16
uriniferous tubule	4.82e-08	16
metanephric mesenchyme	4.82e-08	16
nephrogenic mesenchyme	4.82e-08	16
circulatory system	5.07e-08	113
excretory tube	1.61e-07	17
mesonephric epithelium	1.61e-07	17
mesonephric tubule	1.61e-07	17
nephric duct	1.61e-07	17
kidney epithelium	1.61e-07	17
renal duct	1.61e-07	17
mesonephric duct	1.61e-07	17
pronephric duct	1.61e-07	17
parenchyma	5.11e-07	17
mesonephros	6.42e-07	18
pronephros	6.42e-07	18
nephrogenic cord	6.42e-07	18
pronephric mesoderm	6.42e-07	18
rostral part of nephrogenic cord	6.42e-07	18
presumptive pronephric mesoderm	6.42e-07	18
systemic artery	7.36e-07	33
systemic arterial system	7.36e-07	33
cortex of kidney	8.64e-07	13
renal parenchyma	8.64e-07	13

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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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.