Coexpression cluster:C3013

Full id: C3013_Smooth_Fibroblast_hepatic_mesenchymal_basal_spindle_Mesothelial

Phase1 CAGE Peaks

Hg19::chr10:33247124..33247207,-	p1@ITGB1
Hg19::chr10:33247223..33247234,-	p3@ITGB1
Hg19::chr8:62627160..62627178,-	p2@ASPH

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:0031594	neuromuscular junction	0.0291501513585371
GO:0004597	peptide-aspartate beta-dioxygenase activity	0.0291501513585371
GO:0042383	sarcolemma	0.0291501513585371
GO:0008307	structural constituent of muscle	0.0291501513585371
GO:0001726	ruffle	0.0291501513585371
GO:0016706	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors	0.0291501513585371
GO:0030176	integral to endoplasmic reticulum membrane	0.0291501513585371
GO:0008305	integrin complex	0.0291501513585371
GO:0031227	intrinsic to endoplasmic reticulum membrane	0.0291501513585371
GO:0031252	leading edge	0.0291501513585371
GO:0006968	cellular defense response	0.0291501513585371
GO:0051213	dioxygenase activity	0.0291501513585371
GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	0.0291501513585371
GO:0016701	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen	0.0291501513585371
GO:0048770	pigment granule	0.0291501513585371
GO:0042470	melanosome	0.0291501513585371
GO:0007229	integrin-mediated signaling pathway	0.0291501513585371
GO:0007160	cell-matrix adhesion	0.0301724825008919
GO:0031589	cell-substrate adhesion	0.0301724825008919
GO:0046982	protein heterodimerization activity	0.0301724825008919
GO:0043235	receptor complex	0.0301724825008919
GO:0018193	peptidyl-amino acid modification	0.0316759691239406
GO:0031301	integral to organelle membrane	0.0347967680636087
GO:0031300	intrinsic to organelle membrane	0.0364586862712288
GO:0003012	muscle system process	0.0365254835953352
GO:0006936	muscle contraction	0.0365254835953352
GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	0.0377240214046705
GO:0007156	homophilic cell adhesion	0.0423186472106859
GO:0032501	multicellular organismal process	0.0427628214148144
GO:0016477	cell migration	0.0446564411088571
GO:0009055	electron carrier activity	0.046911570277405

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
fibroblast	1.78e-18	76
muscle precursor cell	1.72e-12	58
myoblast	1.72e-12	58
multi-potent skeletal muscle stem cell	1.72e-12	58
muscle cell	2.88e-11	55
mesodermal cell	1.46e-10	121
embryonic cell	7.84e-10	250
skin fibroblast	2.71e-09	23
smooth muscle cell	3.95e-09	43
smooth muscle myoblast	3.95e-09	43
vascular associated smooth muscle cell	4.05e-09	32
electrically responsive cell	8.85e-09	61
electrically active cell	8.85e-09	61
contractile cell	1.00e-08	59
non-terminally differentiated cell	6.90e-08	106

Uber Anatomy

Ontology term	p-value	n
multi-cellular organism	9.78e-16	656
anatomical system	1.37e-14	624
anatomical group	2.92e-14	625
multilaminar epithelium	6.23e-14	83
surface structure	1.94e-13	99
dense mesenchyme tissue	2.26e-13	73
somite	2.33e-13	71
presomitic mesoderm	2.33e-13	71
presumptive segmental plate	2.33e-13	71
dermomyotome	2.33e-13	71
trunk paraxial mesoderm	2.33e-13	71
paraxial mesoderm	4.01e-13	72
presumptive paraxial mesoderm	4.01e-13	72
organism subdivision	1.34e-12	264
muscle tissue	3.06e-12	64
musculature	3.06e-12	64
musculature of body	3.06e-12	64
skeletal muscle tissue	3.45e-12	62
striated muscle tissue	3.45e-12	62
myotome	3.45e-12	62
splanchnic layer of lateral plate mesoderm	5.33e-12	83
mesenchyme	9.35e-12	160
entire embryonic mesenchyme	9.35e-12	160
unilaminar epithelium	3.14e-11	148
trunk mesenchyme	3.28e-11	122
trunk	1.39e-10	199
epithelial vesicle	2.10e-10	78
artery	6.52e-10	42
arterial blood vessel	6.52e-10	42
arterial system	6.52e-10	42
vasculature	1.34e-09	78
vascular system	1.34e-09	78
epithelial tube open at both ends	2.59e-09	59
blood vessel	2.59e-09	59
blood vasculature	2.59e-09	59
vascular cord	2.59e-09	59
integument	5.97e-09	46
integumental system	5.97e-09	46
systemic artery	8.20e-09	33
systemic arterial system	8.20e-09	33
epithelial tube	1.49e-08	117
mesoderm	2.27e-08	315
mesoderm-derived structure	2.27e-08	315
presumptive mesoderm	2.27e-08	315
vessel	2.93e-08	68
skin of body	2.98e-08	41
circulatory system	8.16e-08	112
cardiovascular system	1.14e-07	109
heart	3.20e-07	24
primitive heart tube	3.20e-07	24
primary heart field	3.20e-07	24
anterior lateral plate mesoderm	3.20e-07	24
heart tube	3.20e-07	24
heart primordium	3.20e-07	24
cardiac mesoderm	3.20e-07	24
cardiogenic plate	3.20e-07	24
heart rudiment	3.20e-07	24
multi-tissue structure	3.60e-07	342
organ component layer	3.73e-07	66
primary circulatory organ	3.98e-07	27
developing anatomical structure	6.14e-07	581
embryo	7.59e-07	592
embryonic structure	8.34e-07	564

Disease

Ontology term	p-value	n
ovarian cancer	1.94e-08	14

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.018904199805915
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0323375850355096
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320212387164658
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0318909780389702
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0459795679563644
ELK4#2005	2	10.823787772312	0.0109128471951648	0.0401680005715026
FOSL2#2355	2	11.2868004030411	0.010053458697312	0.0376550413458816
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127555071459262
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293053795214318
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00307760890116467
REST#5978	3	9.65002871612802	0.00111263624711459	0.00765145301984596
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275264262781838
TFAP2A#7020	2	11.0124229153633	0.0105499065521556	0.0389901160833923
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00612774842974195
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0139561999889548

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.