Coexpression cluster:C1437

Full id: C1437_Mesenchymal_Osteoblast_Renal_Pericytes_Placental_Fibroblast_Nucleus

Phase1 CAGE Peaks

Hg19::chr17:79791135..79791175,-	p1@FAM195B
Hg19::chr19:507487..507508,+	p1@TPGS1
Hg19::chr1:36789194..36789256,-	p1@FAM176B
Hg19::chr1:36789257..36789268,-	p2@FAM176B
Hg19::chr3:49395753..49395769,-	p3@GPX1
Hg19::chr6:144416737..144416766,-	p2@SF3B5

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:0010269	response to selenium ion	0.00356170431735566
GO:0033598	mammary gland epithelial cell proliferation	0.00356170431735566
GO:0033599	regulation of mammary gland epithelial cell proliferation	0.00356170431735566
GO:0008539	proteasome inhibitor activity	0.00356170431735566
GO:0043295	glutathione binding	0.00427398227263908
GO:0008631	induction of apoptosis by oxidative stress	0.00474879929383486
GO:0009650	UV protection	0.00610541935439425
GO:0030503	regulation of cell redox homeostasis	0.00712267470585477
GO:0043154	negative regulation of caspase activity	0.00712267470585477
GO:0042744	hydrogen peroxide catabolic process	0.00771577659443147
GO:0042743	hydrogen peroxide metabolic process	0.00771577659443147
GO:0001836	release of cytochrome c from mitochondria	0.00771577659443147
GO:0004602	glutathione peroxidase activity	0.0083782604577414
GO:0006749	glutathione metabolic process	0.0083782604577414
GO:0008637	apoptotic mitochondrial changes	0.0083782604577414
GO:0017124	SH3 domain binding	0.0083782604577414
GO:0042542	response to hydrogen peroxide	0.0083782604577414
GO:0000302	response to reactive oxygen species	0.0106811811903355
GO:0050678	regulation of epithelial cell proliferation	0.0111441033976822
GO:0009411	response to UV	0.0111441033976822
GO:0050673	epithelial cell proliferation	0.0111441033976822
GO:0010038	response to metal ion	0.0111441033976822
GO:0008629	induction of apoptosis by intracellular signals	0.0111441033976822
GO:0010035	response to inorganic substance	0.0123917946099916
GO:0006800	oxygen and reactive oxygen species metabolic process	0.0123917946099916
GO:0060047	heart contraction	0.0123917946099916
GO:0003015	heart process	0.0123917946099916
GO:0008430	selenium binding	0.0127113856780267
GO:0043281	regulation of caspase activity	0.0147255051928963
GO:0040029	regulation of gene expression, epigenetic	0.0149003678103095
GO:0004601	peroxidase activity	0.0149003678103095
GO:0016684	oxidoreductase activity, acting on peroxide as acceptor	0.0149003678103095
GO:0009416	response to light stimulus	0.0174643995027196
GO:0006790	sulfur metabolic process	0.0175880982868606
GO:0008632	apoptotic program	0.0175880982868606
GO:0007005	mitochondrion organization and biogenesis	0.0175880982868606
GO:0009314	response to radiation	0.0194166461393986
GO:0045454	cell redox homeostasis	0.0202138906401953
GO:0006979	response to oxidative stress	0.0218801128957829
GO:0019904	protein domain specific binding	0.0225752112702164
GO:0005681	spliceosome	0.0241013951022955
GO:0008015	blood circulation	0.0264440662770201
GO:0003013	circulatory system process	0.0264440662770201
GO:0009628	response to abiotic stimulus	0.0266486946639436
GO:0006916	anti-apoptosis	0.0268441119592487
GO:0042277	peptide binding	0.0315119562790315
GO:0006917	induction of apoptosis	0.0315119562790315
GO:0012502	induction of programmed cell death	0.0315119562790315
GO:0008380	RNA splicing	0.0320173688309457
GO:0043066	negative regulation of apoptosis	0.0320173688309457
GO:0043069	negative regulation of programmed cell death	0.0320173688309457
GO:0043065	positive regulation of apoptosis	0.0345455564991135
GO:0043068	positive regulation of programmed cell death	0.0345455564991135
GO:0006397	mRNA processing	0.0358691419109499
GO:0006732	coenzyme metabolic process	0.0371437391052508
GO:0051336	regulation of hydrolase activity	0.0388762339987535
GO:0016071	mRNA metabolic process	0.0419149300765837
GO:0051186	cofactor metabolic process	0.0419149300765837
GO:0019725	cellular homeostasis	0.0450273350297991
GO:0004857	enzyme inhibitor activity	0.0473285241774172

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
mesodermal cell	1.27e-26	121
contractile cell	1.17e-22	59
somatic cell	1.12e-20	588
muscle precursor cell	2.48e-20	58
myoblast	2.48e-20	58
multi-potent skeletal muscle stem cell	2.48e-20	58
muscle cell	2.74e-20	55
electrically responsive cell	5.26e-20	61
electrically active cell	5.26e-20	61
non-terminally differentiated cell	8.52e-19	106
smooth muscle cell	1.01e-16	43
smooth muscle myoblast	1.01e-16	43
vascular associated smooth muscle cell	8.73e-14	32
embryonic cell	1.80e-12	250
multi fate stem cell	1.03e-11	427
somatic stem cell	5.65e-11	433
endothelial cell	1.57e-10	36
stem cell	2.29e-10	441
meso-epithelial cell	4.46e-10	45
fibroblast	6.68e-08	76
lining cell	7.64e-08	58
barrier cell	7.64e-08	58
animal cell	1.16e-07	679
eukaryotic cell	1.16e-07	679

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	8.53e-26	78
somite	2.78e-22	71
presomitic mesoderm	2.78e-22	71
presumptive segmental plate	2.78e-22	71
dermomyotome	2.78e-22	71
trunk paraxial mesoderm	2.78e-22	71
dense mesenchyme tissue	3.43e-22	73
paraxial mesoderm	1.16e-21	72
presumptive paraxial mesoderm	1.16e-21	72
multilaminar epithelium	2.90e-20	83
vasculature	5.77e-19	78
vascular system	5.77e-19	78
skeletal muscle tissue	7.40e-19	62
striated muscle tissue	7.40e-19	62
myotome	7.40e-19	62
mesoderm	1.92e-18	315
mesoderm-derived structure	1.92e-18	315
presumptive mesoderm	1.92e-18	315
muscle tissue	1.37e-17	64
musculature	1.37e-17	64
musculature of body	1.37e-17	64
splanchnic layer of lateral plate mesoderm	1.98e-17	83
vessel	7.22e-16	68
cardiovascular system	3.14e-15	109
epithelial tube open at both ends	3.96e-15	59
blood vessel	3.96e-15	59
blood vasculature	3.96e-15	59
vascular cord	3.96e-15	59
circulatory system	9.18e-15	112
artery	3.96e-14	42
arterial blood vessel	3.96e-14	42
arterial system	3.96e-14	42
musculoskeletal system	1.16e-13	167
mesenchyme	6.44e-13	160
entire embryonic mesenchyme	6.44e-13	160
epithelial tube	1.06e-12	117
unilaminar epithelium	1.58e-12	148
trunk mesenchyme	4.90e-12	122
lateral plate mesoderm	3.09e-11	203
systemic artery	1.29e-10	33
systemic arterial system	1.29e-10	33
trunk	5.98e-08	199
organism subdivision	6.00e-07	264
adipose tissue	9.22e-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
ATF3#467	3	11.2315872630044	0.00159345997118423	0.0100409898594491
CCNT2#905	4	4.22413438464176	0.00710980547887581	0.0296128005746086
EGR1#1958	5	4.15681591234178	0.00161796681886444	0.0101342711164318
ELF1#1997	6	4.25809795880754	0.000167722477628883	0.00205282641990893
ELK4#2005	3	8.11784082923401	0.00405611313418576	0.019408796830442
ETS1#2113	5	8.10730076850195	6.29183579217211e-05	0.00102754188944279
GABPB1#2553	4	4.71178922412145	0.00473005431155596	0.0222894979129447
MXI1#4601	4	6.6410477525062	0.00128851695803914	0.00863911039228667
NFKB1#4790	4	3.65870894946256	0.0120792728901523	0.0438341619657615
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380269059053913
SIN3A#25942	6	5.40888472681514	3.99207083571449e-05	0.000742789748817362
SP1#6667	4	3.7989209187606	0.0105224661679851	0.0389493476561472
SREBF1#6720	2	15.6686164801628	0.00641128316580946	0.0278913651249208
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00573211993726483
TAF7#6879	3	5.71653470246196	0.0109272937988966	0.0402140891878841
THAP1#55145	3	15.6845723014257	0.000602346980086485	0.00503187620006818
ZNF263#10127	4	5.48122775800712	0.00267560938060723	0.0147468451159026

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.