Coexpression cluster:C3859

Full id: C3859_CD14_Fibroblast_Preadipocyte_Smooth_leiomyoma_tenocyte_Myoblast

Phase1 CAGE Peaks

Hg19::chr1:145096387..145096477,+	p1@SEC22B
Hg19::chr1:145116327..145116343,+	p@chr1:145116327..145116343 +
Hg19::chr4:122618095..122618161,-	p1@ANXA5

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:0033116	ER-Golgi intermediate compartment membrane	0.0205762027448468
GO:0050819	negative regulation of coagulation	0.0205762027448468
GO:0050818	regulation of coagulation	0.0205762027448468
GO:0055102	lipase inhibitor activity	0.0205762027448468
GO:0004859	phospholipase inhibitor activity	0.0205762027448468
GO:0006888	ER to Golgi vesicle-mediated transport	0.0332505298680399
GO:0005793	ER-Golgi intermediate compartment	0.0332505298680399
GO:0005544	calcium-dependent phospholipid binding	0.0365310003594502
GO:0048770	pigment granule	0.0405595081249357
GO:0042470	melanosome	0.0405595081249357
GO:0048193	Golgi vesicle transport	0.0405595081249357
GO:0007596	blood coagulation	0.0405595081249357
GO:0050817	coagulation	0.0405595081249357
GO:0007599	hemostasis	0.0405595081249357
GO:0050878	regulation of body fluid levels	0.0442604929895272
GO:0042060	wound healing	0.0442604929895272

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
multi fate stem cell	4.62e-31	427
somatic stem cell	1.62e-29	433
stem cell	3.77e-26	441
somatic cell	1.46e-21	588
muscle precursor cell	5.31e-18	58
myoblast	5.31e-18	58
multi-potent skeletal muscle stem cell	5.31e-18	58
animal cell	7.49e-18	679
eukaryotic cell	7.49e-18	679
muscle cell	1.27e-16	55
connective tissue cell	3.50e-16	361
mesenchymal cell	4.21e-15	354
fibroblast	4.38e-15	76
contractile cell	1.33e-14	59
smooth muscle cell	4.00e-14	43
smooth muscle myoblast	4.00e-14	43
mesodermal cell	5.30e-14	121
native cell	2.36e-13	722
electrically responsive cell	5.99e-13	61
electrically active cell	5.99e-13	61
stuff accumulating cell	1.30e-12	87
defensive cell	2.37e-12	48
phagocyte	2.37e-12	48
vascular associated smooth muscle cell	4.38e-12	32
motile cell	5.52e-12	386
monopoietic cell	1.60e-11	59
monocyte	1.60e-11	59
monoblast	1.60e-11	59
promonocyte	1.60e-11	59
macrophage dendritic cell progenitor	9.79e-11	61
non-terminally differentiated cell	1.39e-10	106
classical monocyte	3.37e-10	42
CD14-positive, CD16-negative classical monocyte	3.37e-10	42
myeloid lineage restricted progenitor cell	4.61e-10	66
granulocyte monocyte progenitor cell	1.69e-08	67
myeloid leukocyte	6.97e-08	72
fat cell	3.76e-07	15

Uber Anatomy

Ontology term	p-value	n
musculoskeletal system	3.07e-27	167
mesoderm	5.72e-22	315
mesoderm-derived structure	5.72e-22	315
presumptive mesoderm	5.72e-22	315
somite	2.27e-16	71
presomitic mesoderm	2.27e-16	71
presumptive segmental plate	2.27e-16	71
dermomyotome	2.27e-16	71
trunk paraxial mesoderm	2.27e-16	71
dense mesenchyme tissue	2.46e-16	73
paraxial mesoderm	4.67e-16	72
presumptive paraxial mesoderm	4.67e-16	72
connective tissue	1.25e-15	371
skeletal muscle tissue	5.99e-15	62
striated muscle tissue	5.99e-15	62
myotome	5.99e-15	62
muscle tissue	2.98e-14	64
musculature	2.98e-14	64
musculature of body	2.98e-14	64
multilaminar epithelium	3.37e-13	83
epithelial vesicle	4.62e-13	78
lateral plate mesoderm	5.75e-12	203
skeletal system	1.34e-11	100
trunk mesenchyme	1.79e-11	122
skeletal element	1.41e-10	90
unilaminar epithelium	5.09e-10	148
bone marrow	6.15e-10	76
artery	1.25e-09	42
arterial blood vessel	1.25e-09	42
arterial system	1.25e-09	42
bone element	5.20e-09	82
systemic artery	7.94e-09	33
systemic arterial system	7.94e-09	33
mesenchyme	1.60e-08	160
entire embryonic mesenchyme	1.60e-08	160
vasculature	3.78e-08	78
vascular system	3.78e-08	78
cardiovascular system	1.79e-07	109
splanchnic layer of lateral plate mesoderm	1.96e-07	83
immune system	2.38e-07	93
vessel	7.60e-07	68

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
SMC3#9126	2	10.0299552299552	0.012665637976747	0.0457489992617238
ZZZ3#26009	1	79.8044041450777	0.012478437908258	0.0451618524690909

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.