Coexpression cluster:C3181

Full id: C3181_Mesenchymal_Smooth_Hair_Aortic_Fibroblast_Hepatic_tridermal

Phase1 CAGE Peaks

Hg19::chr11:6341724..6341760,-	p1@PRKCDBP
Hg19::chr19:48828788..48828853,+	p1@EMP3
Hg19::chr22:38071636..38071652,+	p1@LGALS1

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:0016265	death	0.0394088188776617
GO:0008219	cell death	0.0394088188776617
GO:0045445	myoblast differentiation	0.0394088188776617
GO:0048741	skeletal muscle fiber development	0.0394088188776617
GO:0048747	muscle fiber development	0.0394088188776617
GO:0048468	cell development	0.0394088188776617
GO:0042692	muscle cell differentiation	0.0394088188776617
GO:0007519	skeletal muscle development	0.0487380796564191
GO:0014706	striated muscle development	0.0487380796564191
GO:0048869	cellular developmental process	0.0487380796564191
GO:0030154	cell differentiation	0.0487380796564191
GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB cascade	0.0487380796564191
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.0487380796564191
GO:0048856	anatomical structure development	0.0487380796564191

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
somatic cell	1.68e-40	588
mesodermal cell	1.16e-31	121
animal cell	1.86e-27	679
eukaryotic cell	1.86e-27	679
contractile cell	6.13e-24	59
muscle precursor cell	2.35e-23	58
myoblast	2.35e-23	58
multi-potent skeletal muscle stem cell	2.35e-23	58
muscle cell	1.73e-22	55
fibroblast	6.10e-21	76
smooth muscle cell	5.75e-20	43
smooth muscle myoblast	5.75e-20	43
multi fate stem cell	1.18e-19	427
somatic stem cell	3.69e-19	433
non-terminally differentiated cell	2.76e-18	106
electrically responsive cell	4.12e-18	61
electrically active cell	4.12e-18	61
stem cell	4.00e-17	441
embryonic cell	4.16e-17	250
native cell	1.09e-16	722
vascular associated smooth muscle cell	4.32e-16	32
meso-epithelial cell	7.21e-10	45
endothelial cell	9.35e-10	36
lining cell	1.07e-09	58
barrier cell	1.07e-09	58
skin fibroblast	1.89e-08	23
cardiocyte	1.48e-07	16
connective tissue cell	3.60e-07	361
endothelial cell of vascular tree	4.66e-07	24

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	3.41e-28	78
somite	2.69e-25	71
presomitic mesoderm	2.69e-25	71
presumptive segmental plate	2.69e-25	71
dermomyotome	2.69e-25	71
trunk paraxial mesoderm	2.69e-25	71
dense mesenchyme tissue	9.70e-25	73
paraxial mesoderm	1.78e-24	72
presumptive paraxial mesoderm	1.78e-24	72
vasculature	5.72e-24	78
vascular system	5.72e-24	78
splanchnic layer of lateral plate mesoderm	1.04e-23	83
multilaminar epithelium	1.17e-23	83
mesoderm	7.19e-23	315
mesoderm-derived structure	7.19e-23	315
presumptive mesoderm	7.19e-23	315
vessel	2.52e-22	68
skeletal muscle tissue	1.53e-21	62
striated muscle tissue	1.53e-21	62
myotome	1.53e-21	62
epithelial tube open at both ends	3.67e-21	59
blood vessel	3.67e-21	59
blood vasculature	3.67e-21	59
vascular cord	3.67e-21	59
muscle tissue	1.93e-20	64
musculature	1.93e-20	64
musculature of body	1.93e-20	64
cardiovascular system	5.35e-20	109
artery	2.53e-19	42
arterial blood vessel	2.53e-19	42
arterial system	2.53e-19	42
circulatory system	3.33e-19	112
epithelial tube	6.92e-17	117
unilaminar epithelium	1.28e-16	148
musculoskeletal system	1.95e-16	167
systemic artery	4.36e-15	33
systemic arterial system	4.36e-15	33
trunk mesenchyme	5.66e-15	122
lateral plate mesoderm	4.94e-14	203
mesenchyme	1.37e-13	160
entire embryonic mesenchyme	1.37e-13	160
surface structure	1.45e-09	99
integument	4.17e-09	46
integumental system	4.17e-09	46
organism subdivision	8.22e-09	264
trunk	2.01e-08	199
aorta	2.47e-08	21
aortic system	2.47e-08	21
anatomical group	2.88e-08	625
anatomical system	3.28e-08	624
skin of body	1.55e-07	41
connective tissue	1.83e-07	371
multi-cellular organism	3.71e-07	656

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.