Coexpression cluster:C3123

Full id: C3123_basal_Adipocyte_Preadipocyte_Olfactory_serous_mesenchymal_Smooth

Phase1 CAGE Peaks

Hg19::chr11:18416103..18416118,+	p1@LDHA
Hg19::chr11:18416135..18416147,+	p2@LDHA
Hg19::chr9:14922428..14922432,-	p1@LDHAP4

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:0004459	L-lactate dehydrogenase activity	0.00333608069390478
GO:0019642	anaerobic glycolysis	0.00333608069390478
GO:0004457	lactate dehydrogenase activity	0.00333608069390478
GO:0006100	tricarboxylic acid cycle intermediate metabolic process	0.00800659366537148
GO:0006096	glycolysis	0.0137255891406368
GO:0006007	glucose catabolic process	0.0137255891406368
GO:0019320	hexose catabolic process	0.0137255891406368
GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	0.0137255891406368
GO:0046365	monosaccharide catabolic process	0.0137255891406368
GO:0046164	alcohol catabolic process	0.0137255891406368
GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	0.0137255891406368
GO:0044275	cellular carbohydrate catabolic process	0.0137255891406368
GO:0016052	carbohydrate catabolic process	0.0137255891406368
GO:0006006	glucose metabolic process	0.0137255891406368
GO:0019318	hexose metabolic process	0.0171391145649358
GO:0005996	monosaccharide metabolic process	0.0171391145649358
GO:0006066	alcohol metabolic process	0.0261980454491934
GO:0044262	cellular carbohydrate metabolic process	0.0275490032038769
GO:0044265	cellular macromolecule catabolic process	0.0275490032038769
GO:0005829	cytosol	0.0284234075120688
GO:0009057	macromolecule catabolic process	0.029786434767007
GO:0005975	carbohydrate metabolic process	0.03520290367003
GO:0044248	cellular catabolic process	0.03520290367003
GO:0009056	catabolic process	0.0405750814396169

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
animal cell	2.14e-28	679
eukaryotic cell	2.14e-28	679
somatic cell	3.04e-19	588
native cell	2.57e-17	722
fibroblast	1.72e-13	76
vascular associated smooth muscle cell	1.31e-09	32
stem cell	5.90e-09	441
somatic stem cell	7.04e-09	433
skin fibroblast	7.79e-09	23
multi fate stem cell	1.05e-08	427
non-terminally differentiated cell	3.17e-08	106
embryonic cell	6.33e-08	250
muscle precursor cell	1.66e-07	58
myoblast	1.66e-07	58
multi-potent skeletal muscle stem cell	1.66e-07	58
smooth muscle cell	6.34e-07	43
smooth muscle myoblast	6.34e-07	43
muscle cell	8.89e-07	55

Uber Anatomy

Ontology term	p-value	n
artery	5.30e-11	42
arterial blood vessel	5.30e-11	42
arterial system	5.30e-11	42
integument	1.23e-09	46
integumental system	1.23e-09	46
multilaminar epithelium	4.01e-09	83
unilaminar epithelium	4.98e-09	148
somite	1.08e-08	71
presomitic mesoderm	1.08e-08	71
presumptive segmental plate	1.08e-08	71
dermomyotome	1.08e-08	71
trunk paraxial mesoderm	1.08e-08	71
systemic artery	1.36e-08	33
systemic arterial system	1.36e-08	33
skin of body	1.96e-08	41
surface structure	2.06e-08	99
dense mesenchyme tissue	2.70e-08	73
paraxial mesoderm	3.65e-08	72
presumptive paraxial mesoderm	3.65e-08	72
splanchnic layer of lateral plate mesoderm	1.11e-07	83
trunk	1.15e-07	199
epithelial tube open at both ends	4.12e-07	59
blood vessel	4.12e-07	59
blood vasculature	4.12e-07	59
vascular cord	4.12e-07	59
epithelial vesicle	5.55e-07	78
skeletal muscle tissue	7.61e-07	62
striated muscle tissue	7.61e-07	62
myotome	7.61e-07	62

Disease

Ontology term	p-value	n
disease of cellular proliferation	4.44e-07	239
cancer	7.08e-07	235

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
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.0296107676831855
GTF2B#2959	2	21.2958866228828	0.00287818058991141	0.0155740273887238
HNF4A#3172	2	15.4215269086358	0.00544421048668661	0.0246686580337135
HNF4G#3174	2	19.1689483509645	0.00354398661128422	0.0179666238384502
MAFF#23764	2	37.5435709932968	0.000934477401556032	0.00676762258796965
MAFK#7975	2	18.0671554252199	0.00398367474493681	0.0191050652838525
MEF2A#4205	2	12.495487273096	0.00823502947802974	0.0324734092375287
NR3C1#2908	2	9.98201555411536	0.0127847436554717	0.0460105390294214
RDBP#7936	2	102.425602660017	0.000126437939273122	0.00168260090975352
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.0329709435225185
STAT1#6772	2	13.8043916647995	0.00677093170844408	0.0287435711201606
TAL1#6886	2	19.9124111182935	0.00328717660874055	0.0170081465365496
ZEB1#6935	2	11.2589546783626	0.0101022267664633	0.0377970359412001

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.