Coexpression cluster:C811

Full id: C811_Smooth_Fibroblast_Preadipocyte_Chondrocyte_hepatic_basal_Adipocyte

Phase1 CAGE Peaks

Hg19::chr12:104443890..104443971,-	p1@GLT8D2
Hg19::chr12:99038511..99038575,-	p1@IKBIP
Hg19::chr1:162602244..162602289,+	p1@DDR2
Hg19::chr2:179343268..179343338,-	p1@FKBP7
Hg19::chr2:190044480..190044494,-	p1@COL5A2
Hg19::chr3:52739588..52739621,-	p2@GLT8D1
Hg19::chr5:143550159..143550236,-	p1@YIPF5
Hg19::chr5:54455989..54456019,+	p1@GPX8
Hg19::chr7:128379390..128379447,+	p1@CALU
Hg19::chr7:30066233..30066332,-	p1@FKBP14

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:0005788	endoplasmic reticulum lumen	4.61097154483163e-05
GO:0044432	endoplasmic reticulum part	0.000235163406472688
GO:0005783	endoplasmic reticulum	0.00139924532238113
GO:0003755	peptidyl-prolyl cis-trans isomerase activity	0.00533970528070001
GO:0016859	cis-trans isomerase activity	0.00533970528070001
GO:0016051	carbohydrate biosynthetic process	0.00978051326245874
GO:0005588	collagen type V	0.013117345110061
GO:0031974	membrane-enclosed lumen	0.0169083956011319
GO:0043233	organelle lumen	0.0169083956011319
GO:0043588	skin development	0.0183586078254092
GO:0016758	transferase activity, transferring hexosyl groups	0.0218303482719949
GO:0016853	isomerase activity	0.0235269792804304
GO:0030199	collagen fibril organization	0.0235269792804304
GO:0005583	fibrillar collagen	0.0239659625334093
GO:0006457	protein folding	0.0239659625334093
GO:0005509	calcium ion binding	0.0305126129548744
GO:0031410	cytoplasmic vesicle	0.0308570937043425
GO:0031982	vesicle	0.0308570937043425
GO:0016757	transferase activity, transferring glycosyl groups	0.0308570937043425

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	8.01e-24	76
muscle precursor cell	4.81e-19	58
myoblast	4.81e-19	58
multi-potent skeletal muscle stem cell	4.81e-19	58
non-terminally differentiated cell	9.82e-19	106
muscle cell	8.81e-18	55
mesodermal cell	3.14e-16	121
contractile cell	1.27e-15	59
electrically responsive cell	4.47e-15	61
electrically active cell	4.47e-15	61
smooth muscle cell	3.22e-14	43
smooth muscle myoblast	3.22e-14	43
embryonic cell	1.32e-13	250
vascular associated smooth muscle cell	1.30e-11	32
skin fibroblast	2.49e-11	23
preadipocyte	6.35e-08	12
stromal cell	1.65e-07	28

Uber Anatomy

Ontology term	p-value	n
dense mesenchyme tissue	4.01e-20	73
somite	5.00e-20	71
presomitic mesoderm	5.00e-20	71
presumptive segmental plate	5.00e-20	71
dermomyotome	5.00e-20	71
trunk paraxial mesoderm	5.00e-20	71
paraxial mesoderm	1.61e-19	72
presumptive paraxial mesoderm	1.61e-19	72
multilaminar epithelium	2.34e-19	83
skeletal muscle tissue	4.90e-18	62
striated muscle tissue	4.90e-18	62
myotome	4.90e-18	62
muscle tissue	1.40e-17	64
musculature	1.40e-17	64
musculature of body	1.40e-17	64
epithelial vesicle	1.44e-16	78
unilaminar epithelium	3.18e-15	148
splanchnic layer of lateral plate mesoderm	2.09e-14	83
mesenchyme	3.17e-14	160
entire embryonic mesenchyme	3.17e-14	160
trunk mesenchyme	7.25e-14	122
surface structure	1.03e-13	99
vasculature	2.43e-13	78
vascular system	2.43e-13	78
organism subdivision	6.66e-13	264
artery	2.83e-11	42
arterial blood vessel	2.83e-11	42
arterial system	2.83e-11	42
integument	3.71e-11	46
integumental system	3.71e-11	46
epithelial tube open at both ends	3.81e-11	59
blood vessel	3.81e-11	59
blood vasculature	3.81e-11	59
vascular cord	3.81e-11	59
vessel	8.74e-11	68
multi-cellular organism	2.36e-10	656
trunk	3.57e-10	199
systemic artery	3.83e-10	33
systemic arterial system	3.83e-10	33
skin of body	9.29e-10	41
multi-tissue structure	4.07e-09	342
cardiovascular system	7.21e-09	109
circulatory system	9.15e-09	112
epithelial tube	3.08e-08	117
organ component layer	4.11e-08	66
anatomical system	5.74e-08	624
anatomical group	7.50e-08	625
cell layer	7.93e-08	309
epithelium	2.16e-07	306
anatomical cluster	7.32e-07	373

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	5	3.16810078848132	0.0122715766979429	0.0444810050587048
CEBPB#1051	6	4.78268857549489	0.000520075535673016	0.00450569629781453
GTF2B#2959	3	9.58314898029727	0.0031186316729436	0.0163910610080296
IRF1#3659	5	3.81858187678195	0.00546562857545373	0.0247571142295968
MXI1#4601	4	3.98462865150372	0.0129656298253104	0.0460130284184168
POLR2A#5430	10	2.14745317655807	0.000479337749163792	0.00436532570499802
SIN3A#25942	6	3.24533083608908	0.00422384063048573	0.0201027019507519
TAF1#6872	8	2.67443702859623	0.00155661727806239	0.00988457177014395
TBP#6908	7	2.59473948096747	0.0055886690177364	0.0252738808150763
TRIM28#10155	3	5.57715751357876	0.0140319780523358	0.0492484375376517

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.