Coexpression cluster:C3236

Full id: C3236_Mesenchymal_Endothelial_Smooth_Hair_Fibroblast_Preadipocyte_Renal

Phase1 CAGE Peaks

Hg19::chr12:109915098..109915131,-	p1@KCTD10
Hg19::chr17:40575264..40575282,-	p1@PTRF
Hg19::chr20:35090158..35090240,+	p2@DLGAP4

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:0042134	rRNA primary transcript binding	0.00571041708603294
GO:0006361	transcription initiation from RNA polymerase I promoter	0.00571041708603294
GO:0003716	RNA polymerase I transcription termination factor activity	0.00571041708603294
GO:0003715	transcription termination factor activity	0.00856512133858862
GO:0006353	transcription termination	0.011990110916016
GO:0006360	transcription from RNA polymerase I promoter	0.0142726809766186
GO:0016599	caveolar membrane	0.0225641601782574
GO:0043624	cellular protein complex disassembly	0.0225641601782574
GO:0043241	protein complex disassembly	0.0225641601782574
GO:0032984	macromolecular complex disassembly	0.0225641601782574
GO:0005901	caveola	0.0225641601782574
GO:0019843	rRNA binding	0.025671166149659
GO:0022411	cellular component disassembly	0.0322411709060457

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	2.69e-36	180
mesodermal cell	1.60e-32	119
embryonic cell	6.97e-23	248
fibroblast	2.17e-22	75
contractile cell	3.66e-17	59
muscle precursor cell	2.28e-16	57
myoblast	2.28e-16	57
multi-potent skeletal muscle stem cell	2.28e-16	57
muscle cell	8.83e-16	54
smooth muscle cell	2.25e-15	42
smooth muscle myoblast	2.25e-15	42
lining cell	4.00e-15	57
barrier cell	4.00e-15	57
meso-epithelial cell	2.85e-13	44
vascular associated smooth muscle cell	4.29e-13	32
endothelial cell	5.13e-13	35
electrically responsive cell	7.89e-13	60
electrically active cell	7.89e-13	60
somatic cell	1.61e-12	591
endothelial cell of vascular tree	2.43e-12	24
blood vessel endothelial cell	1.24e-10	18
embryonic blood vessel endothelial progenitor cell	1.24e-10	18
animal cell	7.04e-10	679
eukaryotic cell	7.04e-10	679
skin fibroblast	3.02e-09	23
squamous epithelial cell	1.64e-07	62

Uber Anatomy

Ontology term	p-value	n
vasculature	9.79e-30	79
vascular system	9.79e-30	79
vessel	7.50e-28	69
splanchnic layer of lateral plate mesoderm	3.52e-26	84
blood vessel	1.35e-25	60
epithelial tube open at both ends	1.35e-25	60
blood vasculature	1.35e-25	60
vascular cord	1.35e-25	60
epithelial tube	3.01e-24	118
trunk mesenchyme	4.12e-22	143
somite	8.85e-21	83
paraxial mesoderm	8.85e-21	83
presomitic mesoderm	8.85e-21	83
presumptive segmental plate	8.85e-21	83
trunk paraxial mesoderm	8.85e-21	83
presumptive paraxial mesoderm	8.85e-21	83
artery	1.27e-19	42
arterial blood vessel	1.27e-19	42
arterial system	1.27e-19	42
multilaminar epithelium	1.49e-19	82
cardiovascular system	4.36e-19	110
circulatory system	6.34e-19	113
unilaminar epithelium	6.71e-19	138
trunk	8.65e-19	216
dermomyotome	2.27e-18	70
organism subdivision	1.52e-17	365
cell layer	3.36e-17	312
epithelium	1.71e-16	309
skeletal muscle tissue	1.08e-15	61
striated muscle tissue	1.08e-15	61
myotome	1.08e-15	61
muscle tissue	1.15e-15	63
musculature	1.15e-15	63
musculature of body	1.15e-15	63
multi-cellular organism	1.73e-15	659
systemic artery	7.57e-15	33
systemic arterial system	7.57e-15	33
anatomical cluster	2.35e-14	286
anatomical system	4.68e-14	625
anatomical group	8.54e-14	626
mesenchyme	2.14e-13	238
entire embryonic mesenchyme	2.14e-13	238
surface structure	3.23e-13	95
anatomical conduit	2.16e-12	241
multi-tissue structure	9.17e-12	347
endothelium	1.24e-10	18
blood vessel endothelium	1.24e-10	18
cardiovascular system endothelium	1.24e-10	18
squamous epithelium	3.26e-10	25
simple squamous epithelium	4.00e-10	22
mesoderm	5.11e-10	448
mesoderm-derived structure	5.11e-10	448
presumptive mesoderm	5.11e-10	448
integument	6.21e-10	45
integumental system	6.21e-10	45
aorta	1.52e-09	21
aortic system	1.52e-09	21
skin of body	1.14e-08	40
tube	1.61e-08	194
embryonic structure	2.41e-07	605
developing anatomical structure	2.41e-07	605
germ layer	2.69e-07	604
embryonic tissue	2.69e-07	604
presumptive structure	2.69e-07	604
epiblast (generic)	2.69e-07	604
embryo	6.52e-07	612

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)
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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.