Coexpression cluster:C887

Full id: C887_Mesenchymal_Alveolar_Smooth_Renal_Fibroblast_leiomyoma_Preadipocyte

Phase1 CAGE Peaks

Hg19::chr11:832944..832994,+	p1@CD151
Hg19::chr11:910796..910847,-	p1@CHID1
Hg19::chr16:5121814..5121855,+	p1@ALG1
Hg19::chr17:42148225..42148317,+	p1@G6PC3
Hg19::chr19:10946872..10946894,-	p1@TMED1
Hg19::chr19:3185910..3185962,+	p1@NCLN
Hg19::chr6:33385655..33385719,-	p1@CUTA
Hg19::chr6:44225231..44225280,-	p1@SLC35B2
Hg19::chr8:145582231..145582288,+	p1@GPR172A

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:0044264	cellular polysaccharide metabolic process	0.00742663145894526
GO:0005976	polysaccharide metabolic process	0.00742663145894526
GO:0046964	3'-phosphoadenosine 5'-phosphosulfate transmembrane transporter activity	0.00742663145894526
GO:0004578	chitobiosyldiphosphodolichol beta-mannosyltransferase activity	0.00742663145894526
GO:0046963	3'-phosphoadenosine 5'-phosphosulfate transport	0.00742663145894526
GO:0016020	membrane	0.00742663145894526
GO:0015211	purine nucleoside transmembrane transporter activity	0.00960236620985586
GO:0015860	purine nucleoside transport	0.00960236620985586
GO:0015858	nucleoside transport	0.025594252299723
GO:0012505	endomembrane system	0.0287630402966111
GO:0016021	integral to membrane	0.0287630402966111
GO:0031224	intrinsic to membrane	0.0287630402966111
GO:0006032	chitin catabolic process	0.0287630402966111
GO:0009103	lipopolysaccharide biosynthetic process	0.0287630402966111
GO:0006046	N-acetylglucosamine catabolic process	0.0287630402966111
GO:0006043	glucosamine catabolic process	0.0287630402966111
GO:0008653	lipopolysaccharide metabolic process	0.0287630402966111
GO:0046348	amino sugar catabolic process	0.0287630402966111
GO:0006030	chitin metabolic process	0.0287630402966111
GO:0004568	chitinase activity	0.0287630402966111
GO:0005337	nucleoside transmembrane transporter activity	0.0341983537268676
GO:0044247	cellular polysaccharide catabolic process	0.0341983537268676
GO:0000272	polysaccharide catabolic process	0.0341983537268676
GO:0031090	organelle membrane	0.0341983537268676
GO:0044425	membrane part	0.0341983537268676
GO:0005789	endoplasmic reticulum membrane	0.0341983537268676
GO:0042175	nuclear envelope-endoplasmic reticulum network	0.0341983537268676
GO:0015932	nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity	0.0342014318804026
GO:0000030	mannosyltransferase activity	0.0345857875506221
GO:0044262	cellular carbohydrate metabolic process	0.0345857875506221
GO:0044432	endoplasmic reticulum part	0.0366695653368374
GO:0006044	N-acetylglucosamine metabolic process	0.0393858592285063
GO:0010038	response to metal ion	0.0393858592285063
GO:0006041	glucosamine metabolic process	0.0393858592285063
GO:0033692	cellular polysaccharide biosynthetic process	0.0422531577203064
GO:0000271	polysaccharide biosynthetic process	0.0422531577203064
GO:0006040	amino sugar metabolic process	0.0422531577203064
GO:0010035	response to inorganic substance	0.0422531577203064

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	1.52e-38	180
embryonic cell	4.44e-31	248
animal cell	9.04e-31	679
eukaryotic cell	9.04e-31	679
mesodermal cell	2.01e-25	119
somatic cell	6.42e-22	591
contractile cell	5.46e-21	59
muscle precursor cell	3.98e-19	57
myoblast	3.98e-19	57
multi-potent skeletal muscle stem cell	3.98e-19	57
smooth muscle cell	7.41e-19	42
smooth muscle myoblast	7.41e-19	42
muscle cell	2.44e-18	54
electrically responsive cell	5.14e-17	60
electrically active cell	5.14e-17	60
epithelial cell	1.49e-15	254
vascular associated smooth muscle cell	1.61e-15	32
native cell	1.88e-15	722
fibroblast	2.27e-14	75
lining cell	2.08e-07	57
barrier cell	2.08e-07	57
epithelial cell of nephron	5.51e-07	16

Uber Anatomy

Ontology term	p-value	n
trunk mesenchyme	6.73e-22	143
multilaminar epithelium	9.65e-20	82
trunk	2.24e-19	216
somite	2.26e-19	83
paraxial mesoderm	2.26e-19	83
presomitic mesoderm	2.26e-19	83
presumptive segmental plate	2.26e-19	83
trunk paraxial mesoderm	2.26e-19	83
presumptive paraxial mesoderm	2.26e-19	83
epithelial tube	3.20e-19	118
dermomyotome	1.65e-18	70
vasculature	5.82e-18	79
vascular system	5.82e-18	79
unilaminar epithelium	4.28e-17	138
mesenchyme	5.28e-17	238
entire embryonic mesenchyme	5.28e-17	238
skeletal muscle tissue	2.58e-16	61
striated muscle tissue	2.58e-16	61
myotome	2.58e-16	61
artery	4.14e-16	42
arterial blood vessel	4.14e-16	42
arterial system	4.14e-16	42
splanchnic layer of lateral plate mesoderm	4.83e-16	84
vessel	2.01e-15	69
muscle tissue	3.77e-15	63
musculature	3.77e-15	63
musculature of body	3.77e-15	63
blood vessel	9.84e-15	60
epithelial tube open at both ends	9.84e-15	60
blood vasculature	9.84e-15	60
vascular cord	9.84e-15	60
systemic artery	1.30e-12	33
systemic arterial system	1.30e-12	33
cell layer	2.62e-11	312
cardiovascular system	2.99e-11	110
organism subdivision	3.01e-11	365
multi-tissue structure	5.00e-11	347
epithelium	6.38e-11	309
circulatory system	8.87e-11	113
mesoderm	2.38e-08	448
mesoderm-derived structure	2.38e-08	448
presumptive mesoderm	2.38e-08	448
subdivision of trunk	4.37e-08	113
multi-cellular organism	1.40e-07	659
nephron epithelium	5.51e-07	16
nephron	5.51e-07	16
uriniferous tubule	5.51e-07	16
metanephric mesenchyme	5.51e-07	16
nephrogenic mesenchyme	5.51e-07	16
surface structure	6.76e-07	95
anatomical cluster	7.03e-07	286

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.