Coexpression cluster:C4191

Full id: C4191_Smooth_Mesenchymal_leiomyoma_Fibroblast_Preadipocyte_Adipocyte_Placental

Phase1 CAGE Peaks

Hg19::chr2:220408260..220408340,-	p2@CHPF
Hg19::chr2:220408430..220408555,-	p1@CHPF
Hg19::chr9:139981401..139981451,+	p1@MAN1B1

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:0050510	N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity	0.00718206835348578
GO:0047238	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity	0.00718206835348578
GO:0009311	oligosaccharide metabolic process	0.0157036058276523
GO:0004571	mannosyl-oligosaccharide 1,2-alpha-mannosidase activity	0.0157036058276523
GO:0015924	mannosyl-oligosaccharide mannosidase activity	0.0157036058276523
GO:0008376	acetylgalactosaminyltransferase activity	0.0157036058276523
GO:0015020	glucuronosyltransferase activity	0.0157036058276523
GO:0015923	mannosidase activity	0.0157036058276523
GO:0006487	protein amino acid N-linked glycosylation	0.0211319491565653
GO:0008194	UDP-glycosyltransferase activity	0.0486020383091593
GO:0006486	protein amino acid glycosylation	0.0486020383091593
GO:0043413	biopolymer glycosylation	0.0486020383091593
GO:0009101	glycoprotein biosynthetic process	0.0486020383091593
GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	0.0486020383091593
GO:0009100	glycoprotein metabolic process	0.0492197354072614
GO:0016798	hydrolase activity, acting on glycosyl bonds	0.0492197354072614

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	8.19e-28	180
contractile cell	5.75e-14	59
muscle precursor cell	9.08e-14	57
myoblast	9.08e-14	57
multi-potent skeletal muscle stem cell	9.08e-14	57
embryonic cell	1.43e-13	248
smooth muscle cell	3.49e-13	42
smooth muscle myoblast	3.49e-13	42
muscle cell	7.32e-13	54
electrically responsive cell	2.28e-11	60
electrically active cell	2.28e-11	60
vascular associated smooth muscle cell	9.59e-11	32
fibroblast	1.65e-10	75
epithelial cell	4.90e-07	254
stuff accumulating cell	9.72e-07	39

Uber Anatomy

Ontology term	p-value	n
organism subdivision	7.07e-23	365
trunk	1.88e-17	216
multi-tissue structure	1.26e-15	347
trunk mesenchyme	6.64e-14	143
multilaminar epithelium	3.16e-13	82
mesenchyme	1.81e-12	238
entire embryonic mesenchyme	1.81e-12	238
skeletal muscle tissue	8.34e-12	61
striated muscle tissue	8.34e-12	61
myotome	8.34e-12	61
somite	1.06e-11	83
paraxial mesoderm	1.06e-11	83
presomitic mesoderm	1.06e-11	83
presumptive segmental plate	1.06e-11	83
trunk paraxial mesoderm	1.06e-11	83
presumptive paraxial mesoderm	1.06e-11	83
dermomyotome	2.91e-11	70
muscle tissue	5.17e-11	63
musculature	5.17e-11	63
musculature of body	5.17e-11	63
cell layer	1.40e-10	312
epithelium	1.92e-10	309
primordium	2.29e-10	168
subdivision of trunk	2.92e-08	113
multi-cellular organism	3.18e-08	659
immaterial anatomical entity	6.07e-08	126
organ component layer	6.34e-08	57
extraembryonic membrane	4.47e-07	14
membranous layer	4.47e-07	14
extraembryonic structure	5.70e-07	24
organ part	6.86e-07	219
ectodermal placode	7.67e-07	29

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
BCL3#602	2	23.0314018691589	0.00246467476084291	0.0138570288193191
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.0296343694428565
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190480513634581
CTBP2#1488	2	41.8113335595521	0.000754340825991485	0.00593555349398965
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321407068482444
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463514001202167
ELK4#2005	2	10.823787772312	0.0109128471951648	0.040206259858744
FOSL2#2355	2	11.2868004030411	0.010053458697312	0.0376820690815591
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00392180085099925
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.010891205093438
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.012839337632673
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186989108589982
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295212940255152
NANOG#79923	2	19.4965189873418	0.00342725564850102	0.0174544864033646
NR2C2#7182	2	21.7430739368272	0.00276220797549601	0.015139450997262
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00472135149716132
PBX3#5090	2	14.6096751244961	0.00605612247321789	0.026848432591069
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277486469335011
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247114348528446
SREBF1#6720	3	47.0058494404883	9.62099323994382e-06	0.000255091879407589

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.