Coexpression cluster:C750

Full id: C750_Smooth_Mesenchymal_Fibroblast_Hepatic_Chondrocyte_Lens_tenocyte

Phase1 CAGE Peaks

Hg19::chr12:6937564..6937585,+	p1@LEPREL2
Hg19::chr17:39968182..39968244,-	p1@LEPREL4
Hg19::chr17:39968926..39968976,+	p2@FKBP10
Hg19::chr17:39969232..39969265,+	p1@FKBP10
Hg19::chr19:50031252..50031285,+	p1@RCN3
Hg19::chr19:50031567..50031632,+	p2@RCN3
Hg19::chr1:11994715..11994833,+	p1@PLOD1
Hg19::chr1:12014885..12014920,+	p@chr1:12014885..12014920 +
Hg19::chr1:43232649..43232715,-	p1@LEPRE1
Hg19::chr7:150929550..150929619,+	p1@CHPF2
Hg19::chrX:51636712..51636759,+	p1@MAGED1

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:0031418	L-ascorbic acid binding	6.16739262198812e-07
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	2.05166582405436e-06
GO:0019797	procollagen-proline 3-dioxygenase activity	2.05166582405436e-06
GO:0031544	peptidyl-proline 3-dioxygenase activity	2.05166582405436e-06
GO:0005783	endoplasmic reticulum	2.05166582405436e-06
GO:0051213	dioxygenase activity	4.09714468760063e-06
GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	4.09714468760063e-06
GO:0016701	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen	4.09714468760063e-06
GO:0019798	procollagen-proline dioxygenase activity	5.67381898068508e-06
GO:0031543	peptidyl-proline dioxygenase activity	7.14845068613665e-06
GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	3.27411397309372e-05
GO:0019842	vitamin binding	7.96121713291799e-05
GO:0005788	endoplasmic reticulum lumen	0.00052552777865081
GO:0005506	iron ion binding	0.000584123997613624
GO:0044432	endoplasmic reticulum part	0.000601781767003522
GO:0005737	cytoplasm	0.000932935717654791
GO:0046946	hydroxylysine metabolic process	0.00128537226735743
GO:0046947	hydroxylysine biosynthetic process	0.00128537226735743
GO:0044444	cytoplasmic part	0.00165350468860902
GO:0008475	procollagen-lysine 5-dioxygenase activity	0.00346999433782819
GO:0008285	negative regulation of cell proliferation	0.00401542118850137
GO:0043169	cation binding	0.00767490924381294
GO:0046872	metal ion binding	0.00938806226834687
GO:0016491	oxidoreductase activity	0.00938806226834687
GO:0043167	ion binding	0.00938806226834687
GO:0030867	rough endoplasmic reticulum membrane	0.00978140308676731
GO:0050680	negative regulation of epithelial cell proliferation	0.0102746571907546
GO:0042127	regulation of cell proliferation	0.0128654976873371
GO:0009067	aspartate family amino acid biosynthetic process	0.0130046817132735
GO:0005791	rough endoplasmic reticulum	0.0130046817132735
GO:0044424	intracellular part	0.0130046817132735
GO:0009066	aspartate family amino acid metabolic process	0.0202044284172302
GO:0050678	regulation of epithelial cell proliferation	0.0208221240785165
GO:0043231	intracellular membrane-bound organelle	0.0208221240785165
GO:0043227	membrane-bound organelle	0.0208221240785165
GO:0050673	epithelial cell proliferation	0.0211587578541618
GO:0008283	cell proliferation	0.0240554820540468
GO:0005622	intracellular	0.0245856893432835
GO:0001666	response to hypoxia	0.028377623610498
GO:0019538	protein metabolic process	0.0322888692633528
GO:0031974	membrane-enclosed lumen	0.0353706228375008
GO:0043233	organelle lumen	0.0353706228375008
GO:0043229	intracellular organelle	0.0420348181285098
GO:0043226	organelle	0.0420348181285098
GO:0008652	amino acid biosynthetic process	0.0429255537871426
GO:0048523	negative regulation of cellular process	0.0433668328287759
GO:0003755	peptidyl-prolyl cis-trans isomerase activity	0.0433668328287759
GO:0016859	cis-trans isomerase activity	0.0433668328287759
GO:0048519	negative regulation of biological process	0.0433668328287759
GO:0043170	macromolecule metabolic process	0.0433668328287759

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
mesodermal cell	1.59e-27	121
contractile cell	1.15e-23	59
fibroblast	1.66e-23	76
non-terminally differentiated cell	9.62e-23	106
embryonic cell	1.17e-22	250
muscle precursor cell	1.25e-22	58
myoblast	1.25e-22	58
multi-potent skeletal muscle stem cell	1.25e-22	58
muscle cell	1.10e-21	55
smooth muscle cell	2.37e-19	43
smooth muscle myoblast	2.37e-19	43
electrically responsive cell	4.62e-19	61
electrically active cell	4.62e-19	61
vascular associated smooth muscle cell	1.87e-16	32
somatic cell	2.28e-13	588
animal cell	4.24e-13	679
eukaryotic cell	4.24e-13	679
skin fibroblast	1.94e-08	23
cardiocyte	9.49e-08	16
lining cell	3.79e-07	58
barrier cell	3.79e-07	58
meso-epithelial cell	6.27e-07	45

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	6.18e-25	78
vasculature	7.89e-25	78
vascular system	7.89e-25	78
epithelial tube	2.78e-23	117
mesenchyme	3.95e-23	160
entire embryonic mesenchyme	3.95e-23	160
splanchnic layer of lateral plate mesoderm	7.19e-23	83
unilaminar epithelium	7.28e-23	148
somite	1.44e-22	71
presomitic mesoderm	1.44e-22	71
presumptive segmental plate	1.44e-22	71
dermomyotome	1.44e-22	71
trunk paraxial mesoderm	1.44e-22	71
dense mesenchyme tissue	2.47e-22	73
paraxial mesoderm	7.22e-22	72
presumptive paraxial mesoderm	7.22e-22	72
multilaminar epithelium	4.10e-21	83
skeletal muscle tissue	6.28e-21	62
striated muscle tissue	6.28e-21	62
myotome	6.28e-21	62
trunk mesenchyme	9.95e-21	122
vessel	1.06e-20	68
muscle tissue	9.60e-20	64
musculature	9.60e-20	64
musculature of body	9.60e-20	64
epithelial tube open at both ends	1.10e-19	59
blood vessel	1.10e-19	59
blood vasculature	1.10e-19	59
vascular cord	1.10e-19	59
artery	1.84e-19	42
arterial blood vessel	1.84e-19	42
arterial system	1.84e-19	42
cardiovascular system	1.16e-18	109
circulatory system	1.04e-17	112
trunk	1.14e-17	199
organism subdivision	2.12e-17	264
cell layer	3.39e-16	309
epithelium	1.21e-15	306
systemic artery	2.31e-15	33
systemic arterial system	2.31e-15	33
multi-tissue structure	2.02e-12	342
anatomical cluster	7.57e-12	373
multi-cellular organism	7.58e-12	656
anatomical group	3.17e-09	625
anatomical system	3.33e-09	624
aorta	4.21e-09	21
aortic system	4.21e-09	21
anatomical conduit	9.72e-09	240
integument	2.33e-08	46
integumental system	2.33e-08	46
tube	7.95e-08	192
skin of body	3.06e-07	41
surface structure	3.11e-07	99

Disease

Ontology term	p-value	n
ovarian cancer	5.21e-07	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
FOSL1#8061	3	10.8309762862835	0.00226201738972272	0.0128441708348421
HEY1#23462	8	2.93826257680415	0.00110599738805138	0.00768575828136922
IRF1#3659	5	3.47143806980177	0.00894716207586585	0.0339337131873971
POLR2A#5430	10	1.95223016050734	0.0030407318184143	0.0161350975705401
TAF1#6872	8	2.43130638963294	0.00420424418913911	0.0200176457200592
TBP#6908	7	2.35885407360679	0.011797348605664	0.0429798475957352
ZNF143#7702	5	6.1367620691945	0.000703713135463718	0.00565782110505737
ZNF263#10127	5	3.73720074409576	0.00651090818209497	0.027878838080842

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.