Coexpression cluster:C589

Full id: C589_Mesenchymal_Smooth_Fibroblast_Osteoblast_tenocyte_Preadipocyte_Synoviocyte

Phase1 CAGE Peaks

Hg19::chr11:6411670..6411723,+	p1@SMPD1
Hg19::chr11:65640198..65640281,-	p1@EFEMP2
Hg19::chr11:65640308..65640317,-	p3@EFEMP2
Hg19::chr11:65640325..65640346,-	p2@EFEMP2
Hg19::chr15:74218787..74218813,+	p1@LOXL1
Hg19::chr16:4421841..4421855,+	p1@VASN
Hg19::chr17:46115122..46115173,-	p1@COPZ2
Hg19::chr17:60705021..60705044,+	p1@MRC2
Hg19::chr17:60705055..60705066,+	p3@MRC2
Hg19::chr17:60705074..60705088,+	p2@MRC2
Hg19::chr22:20792089..20792119,-	p1@SCARF2
Hg19::chr22:31503460..31503464,-	p2@ENST00000469262
Hg19::chr22:31503467..31503487,-	p1@ENST00000469262
Hg19::chr8:22446763..22446862,+	p1@PDLIM2

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:0018277	protein amino acid deamination	0.0336747910043565
GO:0006685	sphingomyelin catabolic process	0.0449150536397031
GO:0004720	protein-lysine 6-oxidase activity	0.0449150536397031
GO:0004767	sphingomyelin phosphodiesterase activity	0.0449150536397031
GO:0007157	heterophilic cell adhesion	0.0449150536397031
GO:0005801	cis-Golgi network	0.0449150536397031
GO:0009395	phospholipid catabolic process	0.0449150536397031
GO:0006684	sphingomyelin metabolic process	0.0449150536397031
GO:0030126	COPI vesicle coat	0.0449150536397031
GO:0030663	COPI coated vesicle membrane	0.0449150536397031
GO:0030149	sphingolipid catabolic process	0.0449150536397031
GO:0030137	COPI-coated vesicle	0.0449150536397031
GO:0005578	proteinaceous extracellular matrix	0.0449150536397031

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	6.04e-23	76
non-terminally differentiated cell	3.61e-22	106
contractile cell	2.45e-21	59
muscle precursor cell	2.27e-20	58
myoblast	2.27e-20	58
multi-potent skeletal muscle stem cell	2.27e-20	58
muscle cell	1.82e-19	55
mesodermal cell	5.50e-19	121
electrically responsive cell	9.65e-18	61
electrically active cell	9.65e-18	61
smooth muscle cell	3.64e-17	43
smooth muscle myoblast	3.64e-17	43
vascular associated smooth muscle cell	1.08e-13	32
embryonic cell	2.32e-12	250
skin fibroblast	1.12e-07	23
preadipocyte	6.11e-07	12

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	1.62e-22	78
dense mesenchyme tissue	2.20e-22	73
somite	4.45e-22	71
presomitic mesoderm	4.45e-22	71
presumptive segmental plate	4.45e-22	71
dermomyotome	4.45e-22	71
trunk paraxial mesoderm	4.45e-22	71
paraxial mesoderm	8.88e-22	72
presumptive paraxial mesoderm	8.88e-22	72
multilaminar epithelium	1.85e-20	83
mesenchyme	2.14e-20	160
entire embryonic mesenchyme	2.14e-20	160
skeletal muscle tissue	3.15e-20	62
striated muscle tissue	3.15e-20	62
myotome	3.15e-20	62
muscle tissue	5.75e-20	64
musculature	5.75e-20	64
musculature of body	5.75e-20	64
trunk mesenchyme	2.97e-18	122
splanchnic layer of lateral plate mesoderm	2.92e-17	83
multi-cellular organism	1.33e-16	656
multi-tissue structure	2.30e-16	342
organism subdivision	1.30e-15	264
vasculature	2.77e-15	78
vascular system	2.77e-15	78
unilaminar epithelium	8.60e-15	148
cell layer	2.21e-14	309
anatomical cluster	3.54e-14	373
epithelial tube	3.63e-14	117
epithelium	5.38e-14	306
artery	6.21e-14	42
arterial blood vessel	6.21e-14	42
arterial system	6.21e-14	42
trunk	9.32e-14	199
epithelial tube open at both ends	3.02e-13	59
blood vessel	3.02e-13	59
blood vasculature	3.02e-13	59
vascular cord	3.02e-13	59
anatomical system	8.50e-13	624
anatomical group	1.38e-12	625
vessel	1.87e-12	68
systemic artery	3.58e-12	33
systemic arterial system	3.58e-12	33
circulatory system	1.96e-11	112
cardiovascular system	2.59e-11	109
anatomical conduit	1.67e-08	240
surface structure	3.20e-08	99
developing anatomical structure	7.81e-08	581
embryo	8.41e-08	592
embryonic structure	1.05e-07	564
germ layer	1.40e-07	560
germ layer / neural crest	1.40e-07	560
embryonic tissue	1.40e-07	560
presumptive structure	1.40e-07	560
germ layer / neural crest derived structure	1.40e-07	560
epiblast (generic)	1.40e-07	560
heart	1.66e-07	24
primitive heart tube	1.66e-07	24
primary heart field	1.66e-07	24
anterior lateral plate mesoderm	1.66e-07	24
heart tube	1.66e-07	24
heart primordium	1.66e-07	24
cardiac mesoderm	1.66e-07	24
cardiogenic plate	1.66e-07	24
heart rudiment	1.66e-07	24
integument	1.86e-07	46
integumental system	1.86e-07	46
primary circulatory organ	2.22e-07	27
tube	3.78e-07	192
aorta	8.41e-07	21
aortic system	8.41e-07	21

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
CTBP2#1488	3	12.5434000678656	0.00159612266729121	0.0100541287846337
EGR1#1958	10	3.32545272987342	0.000115549638535482	0.00157154430251428
POLR2A#5430	15	2.14745317655807	1.04920735639056e-05	0.000272650328673983
RAD21#5885	6	4.14201355818253	0.00187629003014743	0.0110598179511552
ZBTB33#10009	3	6.33294500599623	0.0107732645418473	0.0397551047800859
ZNF263#10127	7	3.83685943060498	0.00103612939564987	0.00732798252537932

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.