Coexpression cluster:C562

Full id: C562_Smooth_Fibroblast_Preadipocyte_Hepatic_Alveolar_Adipocyte_Mesenchymal

Phase1 CAGE Peaks

Hg19::chr11:66056544..66056560,-	p4@YIF1A
Hg19::chr11:66056564..66056579,-	p2@YIF1A
Hg19::chr11:68039364..68039457,-	p1@C11orf24
Hg19::chr14:24664776..24664904,-	p3@TM9SF1
Hg19::chr19:4670345..4670382,-	p1@C19orf10
Hg19::chr1:2323260..2323307,+	p1@RER1
Hg19::chr2:220363579..220363641,+	p1@GMPPA
Hg19::chr2:27255806..27255879,+	p1@TMEM214
Hg19::chr3:10362736..10362809,-	p1@SEC13
Hg19::chr3:128968437..128968505,+	p1@COPG
Hg19::chr6:33168637..33168704,+	p1@SLC39A7
Hg19::chr7:6523755..6523829,-	p1@DAGLB p1@KDELR2
Hg19::chr9:136242894..136242905,-	p4@SURF4
Hg19::chr9:136242909..136242953,-	p1@SURF4
Hg19::chr9:136242956..136242976,-	p2@SURF4
Hg19::chrX:54835499..54835584,+	p2@MAGED2

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:0005793	ER-Golgi intermediate compartment	0.00833926739920197
GO:0000139	Golgi membrane	0.00833926739920197
GO:0012505	endomembrane system	0.00833926739920197
GO:0044431	Golgi apparatus part	0.00833926739920197
GO:0044425	membrane part	0.0139153532669686
GO:0016192	vesicle-mediated transport	0.0161922944162981
GO:0031090	organelle membrane	0.0165749186817612
GO:0005794	Golgi apparatus	0.0180427800933964
GO:0016021	integral to membrane	0.0214975997088356
GO:0031224	intrinsic to membrane	0.0214975997088356
GO:0015031	protein transport	0.0227785891077271
GO:0005783	endoplasmic reticulum	0.0227785891077271
GO:0046907	intracellular transport	0.0227785891077271
GO:0045184	establishment of protein localization	0.0227785891077271
GO:0008104	protein localization	0.0227785891077271
GO:0016020	membrane	0.0227785891077271
GO:0033036	macromolecule localization	0.0248064161649225
GO:0006890	retrograde vesicle-mediated transport, Golgi to ER	0.0249997241602398
GO:0051649	establishment of cellular localization	0.0258787183563686
GO:0030126	COPI vesicle coat	0.0258787183563686
GO:0030663	COPI coated vesicle membrane	0.0258787183563686
GO:0051641	cellular localization	0.0258787183563686
GO:0004806	triacylglycerol lipase activity	0.0265426724499683
GO:0030137	COPI-coated vesicle	0.0265426724499683
GO:0006810	transport	0.0272165256352636
GO:0051234	establishment of localization	0.0291079438701855
GO:0006829	zinc ion transport	0.0318924360004973
GO:0005789	endoplasmic reticulum membrane	0.0368909860600387
GO:0051179	localization	0.0368909860600387
GO:0042175	nuclear envelope-endoplasmic reticulum network	0.0369405361170417
GO:0044432	endoplasmic reticulum part	0.0439203538946573
GO:0006886	intracellular protein transport	0.0439649120519745

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
non-terminally differentiated cell	7.89e-42	180
animal cell	3.18e-27	679
eukaryotic cell	3.18e-27	679
contractile cell	5.07e-24	59
mesodermal cell	7.54e-24	119
muscle precursor cell	6.48e-23	57
myoblast	6.48e-23	57
multi-potent skeletal muscle stem cell	6.48e-23	57
embryonic cell	2.08e-22	248
somatic cell	2.72e-22	591
muscle cell	6.44e-22	54
fibroblast	7.08e-21	75
smooth muscle cell	7.30e-21	42
smooth muscle myoblast	7.30e-21	42
electrically responsive cell	3.10e-18	60
electrically active cell	3.10e-18	60
vascular associated smooth muscle cell	4.75e-17	32
native cell	1.16e-11	722
epithelial cell	1.42e-07	254
skin fibroblast	3.10e-07	23
multi fate stem cell	3.96e-07	430
somatic stem cell	5.76e-07	436
cardiocyte	6.45e-07	16

Uber Anatomy

Ontology term	p-value	n
trunk mesenchyme	3.14e-28	143
trunk	1.10e-24	216
somite	1.43e-23	83
paraxial mesoderm	1.43e-23	83
presomitic mesoderm	1.43e-23	83
presumptive segmental plate	1.43e-23	83
trunk paraxial mesoderm	1.43e-23	83
presumptive paraxial mesoderm	1.43e-23	83
epithelial tube	2.48e-23	118
unilaminar epithelium	2.22e-22	138
dermomyotome	2.29e-22	70
multilaminar epithelium	5.34e-22	82
skeletal muscle tissue	9.74e-20	61
striated muscle tissue	9.74e-20	61
myotome	9.74e-20	61
mesenchyme	1.39e-19	238
entire embryonic mesenchyme	1.39e-19	238
muscle tissue	7.89e-19	63
musculature	7.89e-19	63
musculature of body	7.89e-19	63
vasculature	1.45e-18	79
vascular system	1.45e-18	79
splanchnic layer of lateral plate mesoderm	1.46e-17	84
artery	4.30e-17	42
arterial blood vessel	4.30e-17	42
arterial system	4.30e-17	42
vessel	5.90e-16	69
blood vessel	1.68e-15	60
epithelial tube open at both ends	1.68e-15	60
blood vasculature	1.68e-15	60
vascular cord	1.68e-15	60
organism subdivision	6.77e-14	365
systemic artery	1.34e-13	33
systemic arterial system	1.34e-13	33
cardiovascular system	1.91e-12	110
circulatory system	9.08e-12	113
mesoderm	2.06e-11	448
mesoderm-derived structure	2.06e-11	448
presumptive mesoderm	2.06e-11	448
multi-tissue structure	3.00e-11	347
cell layer	3.67e-11	312
epithelium	1.20e-10	309
subdivision of trunk	2.93e-10	113
surface structure	1.68e-09	95
integument	7.57e-09	45
integumental system	7.57e-09	45
multi-cellular organism	1.04e-08	659
anatomical cluster	3.32e-07	286
skin of body	3.44e-07	40
abdominal segment of trunk	3.72e-07	61
abdomen	3.72e-07	61
anatomical group	4.33e-07	626
anatomical system	5.50e-07	625
aorta	7.65e-07	21
aortic system	7.65e-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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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.