Coexpression cluster:C4207

Full id: C4207_Mesenchymal_Fibroblast_Adipocyte_Pancreatic_Trabecular_tenocyte_Hair

Phase1 CAGE Peaks

Hg19::chr2:239756536..239756564,-	p1@BC143627
Hg19::chr2:239756671..239756732,+	p1@TWIST2
Hg19::chr2:239756739..239756755,+	p2@TWIST2

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:0045668	negative regulation of osteoblast differentiation	0.00868362180619333
GO:0045667	regulation of osteoblast differentiation	0.00868362180619333
GO:0001649	osteoblast differentiation	0.0144727030103222
GO:0045596	negative regulation of cell differentiation	0.0202617842144511
GO:0051093	negative regulation of developmental process	0.0202617842144511
GO:0001503	ossification	0.0202617842144511
GO:0031214	biomineral formation	0.0202617842144511
GO:0046849	bone remodeling	0.0202617842144511
GO:0048771	tissue remodeling	0.0202617842144511
GO:0045595	regulation of cell differentiation	0.0250088308018368
GO:0045892	negative regulation of transcription, DNA-dependent	0.0285891548696211
GO:0001501	skeletal development	0.0285891548696211
GO:0016564	transcription repressor activity	0.0285891548696211
GO:0050793	regulation of developmental process	0.0292762106608804
GO:0016481	negative regulation of transcription	0.0325891218373609
GO:0009888	tissue development	0.0325891218373609
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0325891218373609
GO:0031324	negative regulation of cellular metabolic process	0.0367606656462185
GO:0009892	negative regulation of metabolic process	0.039853253763161

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	2.58e-40	180
fibroblast	3.61e-30	75
muscle precursor cell	5.20e-18	57
myoblast	5.20e-18	57
multi-potent skeletal muscle stem cell	5.20e-18	57
muscle cell	1.95e-17	54
contractile cell	3.03e-16	59
electrically responsive cell	7.22e-15	60
electrically active cell	7.22e-15	60
smooth muscle cell	1.01e-14	42
smooth muscle myoblast	1.01e-14	42
skin fibroblast	8.69e-14	23
mesodermal cell	1.14e-11	119
vascular associated smooth muscle cell	1.51e-10	32
fat cell	5.65e-10	15
somatic cell	2.15e-07	591
preadipocyte	3.72e-07	12

Uber Anatomy

Ontology term	p-value	n
somite	1.45e-24	83
paraxial mesoderm	1.45e-24	83
presomitic mesoderm	1.45e-24	83
presumptive segmental plate	1.45e-24	83
trunk paraxial mesoderm	1.45e-24	83
presumptive paraxial mesoderm	1.45e-24	83
dermomyotome	3.11e-22	70
multilaminar epithelium	2.49e-20	82
surface structure	5.69e-19	95
skeletal muscle tissue	1.15e-17	61
striated muscle tissue	1.15e-17	61
myotome	1.15e-17	61
muscle tissue	1.28e-17	63
musculature	1.28e-17	63
musculature of body	1.28e-17	63
integument	9.50e-15	45
integumental system	9.50e-15	45
organism subdivision	3.30e-14	365
trunk mesenchyme	1.06e-13	143
multi-cellular organism	9.03e-13	659
skin of body	4.79e-12	40
anatomical system	5.41e-12	625
anatomical group	9.55e-12	626
trunk	1.06e-11	216
splanchnic layer of lateral plate mesoderm	1.22e-11	84
artery	6.32e-11	42
arterial blood vessel	6.32e-11	42
arterial system	6.32e-11	42
multi-tissue structure	1.56e-09	347
mesenchyme	1.74e-09	238
entire embryonic mesenchyme	1.74e-09	238
adipose tissue	2.02e-09	14
systemic artery	2.02e-09	33
systemic arterial system	2.02e-09	33
blood vessel	4.35e-09	60
epithelial tube open at both ends	4.35e-09	60
blood vasculature	4.35e-09	60
vascular cord	4.35e-09	60
vasculature	5.31e-09	79
vascular system	5.31e-09	79
mesoderm	9.02e-09	448
mesoderm-derived structure	9.02e-09	448
presumptive mesoderm	9.02e-09	448
unilaminar epithelium	2.26e-08	138
vessel	3.75e-07	69
embryonic structure	4.42e-07	605
developing anatomical structure	4.42e-07	605
cardiovascular system	5.24e-07	110
circulatory system	6.17e-07	113
germ layer	6.53e-07	604
embryonic tissue	6.53e-07	604
presumptive structure	6.53e-07	604
epiblast (generic)	6.53e-07	604
cell layer	9.05e-07	312

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
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.011549525087793
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280217858438604
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326313459630847

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.