Coexpression cluster:C1000

Full id: C1000_Osteoblast_Preadipocyte_Hair_Adipocyte_tenocyte_Mesenchymal_leiomyoma

Phase1 CAGE Peaks

Hg19::chr11:65638757..65638772,-	p4@EFEMP2
Hg19::chr16:4431039..4431055,+	p3@VASN
Hg19::chr1:1288794..1288843,-	p@chr1:1288794..1288843 -
Hg19::chr1:1289264..1289283,-	p@chr1:1289264..1289283 -
Hg19::chr1:1289610..1289617,-	p6@MXRA8
Hg19::chr1:1289800..1289816,-	p11@MXRA8
Hg19::chr1:1290090..1290114,-	p4@MXRA8
Hg19::chr3:124560257..124560266,-	p@chr3:124560257..124560266 -

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:0005604	basement membrane	0.0432155128362482
GO:0007596	blood coagulation	0.0432155128362482
GO:0050817	coagulation	0.0432155128362482
GO:0007599	hemostasis	0.0432155128362482
GO:0005201	extracellular matrix structural constituent	0.0432155128362482
GO:0050878	regulation of body fluid levels	0.0432155128362482
GO:0042060	wound healing	0.0432155128362482
GO:0044420	extracellular matrix part	0.0432155128362482

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
fibroblast	1.27e-25	76
contractile cell	5.54e-15	59
muscle precursor cell	1.96e-14	58
myoblast	1.96e-14	58
multi-potent skeletal muscle stem cell	1.96e-14	58
multi fate stem cell	1.28e-13	427
muscle cell	3.86e-13	55
somatic stem cell	5.68e-13	433
stem cell	1.18e-12	441
non-terminally differentiated cell	2.45e-12	106
smooth muscle cell	5.01e-11	43
smooth muscle myoblast	5.01e-11	43
electrically responsive cell	6.74e-11	61
electrically active cell	6.74e-11	61
skin fibroblast	1.74e-10	23
preadipocyte	2.31e-10	12
somatic cell	1.09e-09	588
vascular associated smooth muscle cell	1.29e-08	32
extraembryonic cell	8.33e-08	19
connective tissue cell	1.82e-07	361

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	5.82e-16	78
dense mesenchyme tissue	6.58e-16	73
somite	8.86e-16	71
presomitic mesoderm	8.86e-16	71
presumptive segmental plate	8.86e-16	71
dermomyotome	8.86e-16	71
trunk paraxial mesoderm	8.86e-16	71
paraxial mesoderm	2.73e-15	72
presumptive paraxial mesoderm	2.73e-15	72
muscle tissue	2.39e-13	64
musculature	2.39e-13	64
musculature of body	2.39e-13	64
skeletal muscle tissue	4.76e-13	62
striated muscle tissue	4.76e-13	62
myotome	4.76e-13	62
multilaminar epithelium	1.19e-12	83
trunk mesenchyme	2.66e-12	122
mesenchyme	6.83e-12	160
entire embryonic mesenchyme	6.83e-12	160
organ component layer	1.27e-11	66
organism subdivision	6.08e-10	264
integument	2.30e-09	46
integumental system	2.30e-09	46
surface structure	6.34e-09	99
mesoderm	1.04e-08	315
mesoderm-derived structure	1.04e-08	315
presumptive mesoderm	1.04e-08	315
trunk	1.71e-08	199
skin of body	6.29e-08	41
extraembryonic membrane	1.82e-07	14
membranous layer	1.82e-07	14
connective tissue	2.94e-07	371
splanchnic layer of lateral plate mesoderm	3.46e-07	83
adipose tissue	4.26e-07	14
tissue	7.35e-07	773

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.