Coexpression cluster:C385

Full id: C385_Mesenchymal_Alveolar_Osteoblast_Smooth_Renal_Placental_Fibroblast

Phase1 CAGE Peaks

Hg19::chr11:129903123..129903147,-	p1@TCEB2P2
Hg19::chr11:63993738..63993778,+	p1@NUDT22
Hg19::chr11:64052114..64052210,-	p1@BAD
Hg19::chr11:64085563..64085736,+	p1@PRDX5
Hg19::chr11:6633406..6633456,-	p1@TAF10
Hg19::chr14:94595896..94595949,-	p1@IFI27L2
Hg19::chr15:44084503..44084563,+	p1@SERF2
Hg19::chr16:1401799..1401896,-	p1@C16orf42
Hg19::chr16:2827261..2827299,-	p1@TCEB2
Hg19::chr16:30905311..30905428,-	p1@BCL7C
Hg19::chr17:3571887..3571918,-	p2@TAX1BP3
Hg19::chr17:79849591..79849644,+	p1@ANAPC11
Hg19::chr19:14682838..14682894,-	p1@NDUFB7
Hg19::chr19:17622415..17622481,+	p1@PGLS
Hg19::chr19:19030157..19030210,-	p1@COPE
Hg19::chr19:4124133..4124149,-	p2@MAP2K2
Hg19::chr19:51014430..51014455,-	p2@JOSD2
Hg19::chr19:51014460..51014503,-	p1@JOSD2
Hg19::chr19:7745708..7745752,+	p1@TRAPPC5
Hg19::chr22:20307537..20307590,-	p1@DGCR6L
Hg19::chr22:41985798..41985852,-	p1@PMM1
Hg19::chr3:49395773..49395819,-	p1@GPX1
Hg19::chr3:9834088..9834176,-	p1@TADA3
Hg19::chr7:100861427..100861471,+	p1@ZNHIT1
Hg19::chr7:100888337..100888377,-	p1@FIS1
Hg19::chr7:100888385..100888396,-	p3@FIS1
Hg19::chr9:139743853..139743878,+	p1@PHPT1
Hg19::chr9:140446314..140446398,+	p1@MRPL41

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:0005739	mitochondrion	0.00620645344517677
GO:0005737	cytoplasm	0.00761501180775182
GO:0044444	cytoplasmic part	0.00761501180775182
GO:0006915	apoptosis	0.00761501180775182
GO:0012501	programmed cell death	0.00761501180775182
GO:0016265	death	0.00761501180775182
GO:0008219	cell death	0.00761501180775182
GO:0043231	intracellular membrane-bound organelle	0.00772619952853591
GO:0043227	membrane-bound organelle	0.00772619952853591
GO:0044429	mitochondrial part	0.012211775933763
GO:0010269	response to selenium ion	0.0180924827404877
GO:0048468	cell development	0.0180924827404877
GO:0004601	peroxidase activity	0.0180924827404877
GO:0016684	oxidoreductase activity, acting on peroxide as acceptor	0.0180924827404877
GO:0005741	mitochondrial outer membrane	0.019637546591411
GO:0033598	mammary gland epithelial cell proliferation	0.019637546591411
GO:0008539	proteasome inhibitor activity	0.019637546591411
GO:0033599	regulation of mammary gland epithelial cell proliferation	0.019637546591411
GO:0008969	phosphohistidine phosphatase activity	0.019637546591411
GO:0008632	apoptotic program	0.019637546591411
GO:0007005	mitochondrion organization and biogenesis	0.019637546591411
GO:0031968	organelle outer membrane	0.019637546591411
GO:0019867	outer membrane	0.019637546591411
GO:0044424	intracellular part	0.019637546591411
GO:0042579	microbody	0.019637546591411
GO:0005777	peroxisome	0.019637546591411
GO:0031966	mitochondrial membrane	0.019637546591411
GO:0043295	glutathione binding	0.019637546591411
GO:0017057	6-phosphogluconolactonase activity	0.019637546591411
GO:0000266	mitochondrial fission	0.019637546591411
GO:0019307	mannose biosynthetic process	0.019637546591411
GO:0004615	phosphomannomutase activity	0.019637546591411
GO:0005740	mitochondrial envelope	0.021381196836168
GO:0006979	response to oxidative stress	0.0226387669961546
GO:0044455	mitochondrial membrane part	0.0226387669961546
GO:0008631	induction of apoptosis by oxidative stress	0.0226387669961546
GO:0031307	integral to mitochondrial outer membrane	0.0226387669961546
GO:0031306	intrinsic to mitochondrial outer membrane	0.0272464569702817
GO:0043229	intracellular organelle	0.0272464569702817
GO:0043226	organelle	0.0272464569702817
GO:0048869	cellular developmental process	0.0272988937719487
GO:0030154	cell differentiation	0.0272988937719487
GO:0009650	UV protection	0.0272988937719487
GO:0016559	peroxisome fission	0.0272988937719487
GO:0051920	peroxiredoxin activity	0.0272988937719487
GO:0032592	integral to mitochondrial membrane	0.0272988937719487
GO:0048285	organelle fission	0.034862420969153
GO:0030503	regulation of cell redox homeostasis	0.034862420969153
GO:0043154	negative regulation of caspase activity	0.0384090722914862
GO:0031967	organelle envelope	0.0388818993684594
GO:0031975	envelope	0.0388818993684594
GO:0006368	RNA elongation from RNA polymerase II promoter	0.0402033875658268
GO:0006917	induction of apoptosis	0.0431027183745183
GO:0012502	induction of programmed cell death	0.0431027183745183
GO:0006890	retrograde vesicle-mediated transport, Golgi to ER	0.0431027183745183
GO:0042744	hydrogen peroxide catabolic process	0.0431027183745183
GO:0044446	intracellular organelle part	0.0431027183745183
GO:0044422	organelle part	0.0431027183745183
GO:0005794	Golgi apparatus	0.0431027183745183
GO:0001836	release of cytochrome c from mitochondria	0.0431027183745183
GO:0006740	NADPH regeneration	0.0431027183745183
GO:0006098	pentose-phosphate shunt	0.0431027183745183
GO:0042743	hydrogen peroxide metabolic process	0.0431027183745183
GO:0005515	protein binding	0.0443883691234917
GO:0006013	mannose metabolic process	0.0443883691234917
GO:0005762	mitochondrial large ribosomal subunit	0.0443883691234917
GO:0030663	COPI coated vesicle membrane	0.0443883691234917
GO:0000315	organellar large ribosomal subunit	0.0443883691234917
GO:0030126	COPI vesicle coat	0.0443883691234917
GO:0005779	integral to peroxisomal membrane	0.0443883691234917
GO:0031231	intrinsic to peroxisomal membrane	0.0443883691234917
GO:0004602	glutathione peroxidase activity	0.0443883691234917
GO:0065003	macromolecular complex assembly	0.0443883691234917
GO:0043065	positive regulation of apoptosis	0.0443883691234917
GO:0005622	intracellular	0.0443883691234917
GO:0006891	intra-Golgi vesicle-mediated transport	0.0443883691234917
GO:0030137	COPI-coated vesicle	0.0443883691234917
GO:0006739	NADP metabolic process	0.0443883691234917
GO:0005680	anaphase-promoting complex	0.0443883691234917
GO:0043068	positive regulation of programmed cell death	0.0443883691234917
GO:0030178	negative regulation of Wnt receptor signaling pathway	0.0457598392455279
GO:0006354	RNA elongation	0.0457598392455279
GO:0031090	organelle membrane	0.0457598392455279
GO:0019318	hexose metabolic process	0.0457863884821124
GO:0006749	glutathione metabolic process	0.0457888876222452
GO:0008637	apoptotic mitochondrial changes	0.0457888876222452
GO:0005996	monosaccharide metabolic process	0.0457888876222452
GO:0022607	cellular component assembly	0.0463276222825077
GO:0042542	response to hydrogen peroxide	0.0463276222825077
GO:0017124	SH3 domain binding	0.0463276222825077
GO:0000152	nuclear ubiquitin ligase complex	0.0476122033922862
GO:0006732	coenzyme metabolic process	0.0476122033922862

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	1.69e-24	121
embryonic cell	5.87e-23	250
contractile cell	1.19e-21	59
muscle precursor cell	8.98e-20	58
myoblast	8.98e-20	58
multi-potent skeletal muscle stem cell	8.98e-20	58
muscle cell	2.53e-19	55
electrically responsive cell	1.64e-18	61
electrically active cell	1.64e-18	61
smooth muscle cell	7.26e-18	43
smooth muscle myoblast	7.26e-18	43
non-terminally differentiated cell	3.45e-17	106
somatic cell	2.86e-15	588
vascular associated smooth muscle cell	3.09e-14	32
animal cell	2.62e-10	679
eukaryotic cell	2.62e-10	679
meso-epithelial cell	4.61e-07	45

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	2.39e-25	78
multilaminar epithelium	2.15e-22	83
dense mesenchyme tissue	3.67e-22	73
somite	3.74e-22	71
presomitic mesoderm	3.74e-22	71
presumptive segmental plate	3.74e-22	71
dermomyotome	3.74e-22	71
trunk paraxial mesoderm	3.74e-22	71
paraxial mesoderm	9.24e-22	72
presumptive paraxial mesoderm	9.24e-22	72
skeletal muscle tissue	1.01e-19	62
striated muscle tissue	1.01e-19	62
myotome	1.01e-19	62
muscle tissue	1.58e-18	64
musculature	1.58e-18	64
musculature of body	1.58e-18	64
unilaminar epithelium	5.75e-18	148
mesenchyme	2.89e-17	160
entire embryonic mesenchyme	2.89e-17	160
organism subdivision	6.36e-17	264
trunk mesenchyme	6.49e-17	122
splanchnic layer of lateral plate mesoderm	1.04e-15	83
vasculature	1.65e-15	78
vascular system	1.65e-15	78
epithelial tube	1.98e-15	117
trunk	2.75e-15	199
epithelial tube open at both ends	3.72e-13	59
blood vessel	3.72e-13	59
blood vasculature	3.72e-13	59
vascular cord	3.72e-13	59
circulatory system	3.84e-13	112
artery	4.75e-13	42
arterial blood vessel	4.75e-13	42
arterial system	4.75e-13	42
vessel	6.60e-13	68
cardiovascular system	1.94e-12	109
epithelium	2.55e-12	306
cell layer	2.96e-12	309
multi-tissue structure	1.07e-10	342
systemic artery	1.79e-09	33
systemic arterial system	1.79e-09	33
compound organ	2.85e-07	68
mesoderm	4.12e-07	315
mesoderm-derived structure	4.12e-07	315
presumptive mesoderm	4.12e-07	315
anatomical cluster	4.89e-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
ATF3#467	11	8.82481856378915	1.43387867415765e-08	1.05311430977743e-06
BCL3#602	6	7.40295060080107	0.000127640880360487	0.00169774400203374
BRCA1#672	6	4.32519228069081	0.00216403146497447	0.0124887706343852
CCNT2#905	18	4.07327244233312	9.59358390300145e-09	7.30280108779569e-07
CHD2#1106	11	4.06372325626019	3.0800601802331e-05	0.000628155448473666
CTCF#10664	11	2.10581500370805	0.0088321798606111	0.0335341561225275
CTCFL#140690	6	4.23138736263736	0.00241671280905517	0.0136203696003947
E2F1#1869	21	3.68054191115949	8.0805550823931e-10	7.61665245713045e-08
E2F4#1874	10	4.52430725545873	3.24655435082012e-05	0.000646334140002483
E2F6#1876	19	3.40449853222323	5.14126400499946e-08	3.28408851020268e-06
EBF1#1879	10	3.18088101663179	0.000611820682035375	0.00507892379072351
EGR1#1958	17	3.0285373075633	2.93467489205549e-06	0.000100621966858629
ELF1#1997	27	4.10602303170727	2.20897816274713e-16	4.35289566677637e-14
ELK4#2005	14	8.11784082923401	1.97056937882904e-10	2.04170927932069e-08
ETS1#2113	14	4.86438046110117	1.43855917730337e-07	8.13436285427105e-06
GABPB1#2553	19	4.79592831740933	1.37311896916134e-10	1.46333849000246e-08
GTF2F1#2962	11	5.00486677301193	4.22018104532828e-06	0.000133723145689636
HEY1#23462	25	3.60724200277296	9.9905814499289e-13	1.40620800006621e-10
HMGN3#9324	20	5.84181980239328	6.40409087271727e-13	9.2380779924823e-11
IRF1#3659	21	5.72787281517293	1.32840550682668e-13	2.05536804040699e-11
JUNB#3726	4	4.37294752283159	0.0124508617901381	0.0450698583980394
JUND#3727	10	2.49809426495394	0.00393988024873218	0.0189411320796051
MAX#4149	19	4.3785198096834	6.78038983874354e-10	6.46110524058883e-08
MXI1#4601	19	6.75963789094381	2.99585529287429e-13	4.45703890217233e-11
MYC#4609	19	3.54369127002067	2.60507211470082e-08	1.80658118583824e-06
NFE2#4778	4	11.0291800930899	0.000448481486746233	0.00417273567877861
NFKB1#4790	18	3.52804077269604	9.69991054743024e-08	5.71375610639068e-06
NFYA#4800	6	3.94833872139226	0.00341413065944427	0.0173986723890749
NFYB#4801	7	4.18994831338411	0.00104378784221927	0.00738014748179126
NRF1#4899	14	6.10513972385545	8.03437919924525e-09	6.20179252912029e-07
PAX5#5079	15	3.57298153455955	2.28797339117745e-06	8.15819914650672e-05
POLR2A#5430	27	2.07075842025242	1.68055752509302e-08	1.21716884440492e-06
POU2F2#5452	8	2.60174973078358	0.00868549016408329	0.0330035985900198
RFX5#5993	8	3.44226023634146	0.00153503029532216	0.00975995549818284
SIN3A#25942	23	4.44301245416958	5.07578508488072e-13	7.38314649693394e-11
SIX5#147912	10	6.10239834123536	2.31496312516378e-06	8.22915023243637e-05
SMARCB1#6598	6	3.91129623881945	0.00357718141864032	0.0181208347568209
SMARCC2#6601	4	13.4507677752711	0.000211902498885989	0.00246418940888028
SMC3#9126	7	3.76123321123321	0.00195271160160586	0.0114695037939438
SP1#6667	18	3.66324517166201	5.31869636707385e-08	3.37677404182873e-06
SP2#6668	7	6.53838262346116	6.93660950737152e-05	0.00110032284377335
SPI1#6688	9	2.63710398488231	0.00463907802945849	0.0219022951186029
SRF#6722	10	4.92756366505993	1.54598667385094e-05	0.000362508536664387
STAT1#6772	6	4.43712589225697	0.00190160371755524	0.011191344001902
STAT3#6774	7	2.62986624928856	0.0138135532634627	0.0485912323773249
TAF1#6872	26	3.10425726533491	4.49895909605899e-12	5.9177177460114e-10
TAF7#6879	12	4.89988688782453	1.59055383094714e-06	6.04717333637744e-05
TBP#6908	24	3.17723201751119	1.36020450705771e-10	1.45253986209202e-08
TCF12#6938	8	3.03841854348183	0.00338548980155111	0.0172864559198297
TCF7L2#6934	8	3.07719330375353	0.00312799893625658	0.0164386394054094
THAP1#55145	13	14.5642457084667	8.282200471912e-13	1.17684997970887e-10
USF1#7391	14	3.18074963860398	2.47551898685609e-05	0.000536280289293224
USF2#7392	12	5.56808459360125	4.04862539498964e-07	1.94944392635926e-05
YY1#7528	24	4.20957492844616	2.20226274778884e-13	3.31893389778238e-11
ZBTB33#10009	5	5.65441518392521	0.0016790121056849	0.0104946044231029
ZBTB7A#51341	17	4.46365922263894	8.83684393123115e-09	6.77117493275019e-07
ZNF143#7702	10	4.82174162579568	1.86874630066648e-05	0.000424282597598492

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.