Gene info: ID 864

Gene: RUNX3

GENE ID: 864

Synonyms: AML2|CBFA3|PEBP2aC

Description: runt related transcription factor 3

Gene type: protein-coding

Location: 1p36.11

dbXrefs: Ensembl:ENSG00000020633 MIM:600210 Vega:OTTHUMG00000003316 UniprotKB:Q13761

RefSeq: NC_000001.11

Retrived from: PubMed

SNPs: 0 ANCO-SNPs

Phenotype: ND

# Publications: 13

Sherlock p-value : NA (AD) NA (ND) (Frontal_Cortex)

Pascal p-value : 2.684e-1 (AD) 9.144e-1 (ND)

DNA Methylation

Probe	Locus(GRCh37)	Gene	Region	p-val	Trait	PubMed ID
cg15963463	chr1:25253237	RUNX3		7.160e-13	Maternal smoking in pregnancy	27040690
cg24019564	chr1:25257566	RUNX3		8.330e-14	Maternal smoking in pregnancy	27040690
cg07996594	chr1:25257505	RUNX3		1.460e-9	Maternal smoking in pregnancy	27040690
cg15014975	chr1:25257547	RUNX3		4.100e-11	Maternal smoking in pregnancy	27040690
cg10993442	chr1:25257587	RUNX3		7.750e-9	Maternal smoking in pregnancy	27040690
cg15963463	chr1:25253237	RUNX3		1.510e-14	Maternal smoking in pregnancy	27040690
cg24019564	chr1:25257566	RUNX3		1.280e-13	Maternal smoking in pregnancy	27040690
cg07996594	chr1:25257505	RUNX3		2.000e-12	Maternal smoking in pregnancy	27040690
cg15014975	chr1:25257547	RUNX3		3.230e-12	Maternal smoking in pregnancy	27040690
cg10993442	chr1:25257587	RUNX3		4.560e-8	Maternal smoking in pregnancy	27040690
cg05656688	chr1:25254088	RUNX3		8.380e-8	Maternal smoking in pregnancy	27040690
cg15963463	chr1:25253237	RUNX3		4.120e-12	Maternal smoking in pregnancy	27040690
cg24019564	chr1:25257566	RUNX3		3.910e-11	Maternal smoking in pregnancy	27040690
cg07996594	chr1:25257505	RUNX3		6.140e-12	Maternal smoking in pregnancy	27040690
cg15014975	chr1:25257547	RUNX3		4.240e-8	Maternal smoking in pregnancy	27040690
cg10951873	chr1:25254746	RUNX3		1.000e-13	Smoking	27651444
cg10993442	chr1:25257587	RUNX3		1.800e-9	Smoking	27651444
cg20695936	chr1:25257624	RUNX3		8.000e-9	Smoking	27651444
cg15963463	chr1:25253237	RUNX3		5.300e-8	Smoking	27651444
cg24019564	chr1:25257566	RUNX3		7.300e-8	Smoking	27651444
ch.1.839062R	chr1:25282539	RUNX3		7.010e-8	Tobacco smoking	28225026

Gene Expression in Different Tissues

Temporal and Spatial Expressions (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes average value of the expressions.

Top Co-expressed Genes in Brain-Frontal Cortex (BA9) (GTEx v7)

Top 10 positively co-expressed genes

Gene Symbol	Pearson Correlation Coefficient
STX11	0.814
IL2RG	0.811
PLEKHG2	0.805
PPP1R18	0.804
SH2D2A	0.803
CASP4	0.8
TES	0.8
TEAD2	0.799
TOR4A	0.798
VASP	0.796

Top 10 negatively co-expressed genes

Gene Symbol	Pearson Correlation Coefficient
SVOP	-0.596
MARCH4	-0.587
AMER3	-0.582
CHRNB2	-0.582
ST6GALNAC5	-0.577
KCNB2	-0.573
LRTM2	-0.567
SLC7A4	-0.566
BCL11A	-0.563
PTPRR	-0.563

There is no DrugBank record for this gene !

ID	Drug Name	Action	PubMed
C009505	4,4'-diaminodiphenylmethane	"4,4'-diaminodiphenylmethane results in decreased expression of RUNX3 mRNA"	18648102
C459179	4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	"[NOG protein co-treated with entinostat co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of RUNX3 mRNA"	27188386
C459179	4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	"[NOG protein co-treated with panobinostat co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of RUNX3 mRNA"	27188386
C459179	4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	"[NOG protein co-treated with Valproic Acid co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of RUNX3 mRNA"	27188386
C517041	(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	"(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II) results in decreased expression of RUNX3 mRNA"	19561079
C035207	4-amino-2,6-dinitrotoluene	"4-amino-2,6-dinitrotoluene affects the expression of RUNX3 mRNA"	21346803
C516138	(6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine	"[NOG protein co-treated with entinostat co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of RUNX3 mRNA"	27188386
C516138	(6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine	"[NOG protein co-treated with panobinostat co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of RUNX3 mRNA"	27188386
C516138	(6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine	"[NOG protein co-treated with Valproic Acid co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of RUNX3 mRNA"	27188386
D000082	Acetaminophen	Acetaminophen affects the expression of RUNX3 mRNA	17562736
D016604	Aflatoxin B1	Aflatoxin B1 results in decreased expression of RUNX3 mRNA	28458013
D016604	Aflatoxin B1	Aflatoxin B1 results in increased methylation of RUNX3 gene	27153756\|2845801
D016604	Aflatoxin B1	decitabine inhibits the reaction [Aflatoxin B1 results in decreased expression of RUNX3 mRNA]	28458013
D000643	Ammonium Chloride	Ammonium Chloride affects the expression of RUNX3 mRNA	16483693
D000666	Amphotericin B	Amphotericin B results in decreased expression of RUNX3 mRNA	20849824
D018501	Antirheumatic Agents	Antirheumatic Agents results in decreased expression of RUNX3 mRNA	24449571
D001151	Arsenic	Arsenic affects the methylation of RUNX3 gene	25304211
C015001	arsenite	arsenite results in decreased methylation of RUNX3 promoter	23974009
D001374	Azacitidine	Azacitidine affects the methylation of RUNX3 gene	18058463
D019324	beta-Naphthoflavone	[Diethylnitrosamine co-treated with beta-Naphthoflavone] results in increased expression of RUNX3 mRNA	18164116
D001564	Benzo(a)pyrene	Benzo(a)pyrene results in increased expression of RUNX3 mRNA	20064835
D004958	Estradiol	[Estradiol binds to ESR2 protein] which results in increased expression of RUNX3 mRNA	20404318
C006780	bisphenol A	bisphenol A affects the expression of RUNX3 mRNA	21786754
C006780	bisphenol A	bisphenol A affects the methylation of RUNX3 promoter	27334623
C006780	bisphenol A	bisphenol A results in decreased expression of RUNX3 mRNA	25594700
C006780	bisphenol A	bisphenol A results in decreased methylation of RUNX3 promoter	27312807
C006780	bisphenol A	bisphenol A results in decreased expression of RUNX3 mRNA	25181051
D003471	Cuprizone	Cuprizone results in increased expression of RUNX3 mRNA	27523638
D003520	Cyclophosphamide	Cyclophosphamide results in decreased expression of RUNX3 mRNA	20849824
C014347	decitabine	decitabine affects the expression of RUNX3 mRNA	23300844
C014347	decitabine	decitabine affects the methylation of RUNX3 promoter	17488656\|1757124
C014347	decitabine	decitabine inhibits the reaction [Aflatoxin B1 results in decreased expression of RUNX3 mRNA]	28458013
C014347	decitabine	decitabine results in increased expression of RUNX3 mRNA	16367923\|1908768
D003976	Diazinon	Diazinon results in increased methylation of RUNX3 gene	22964155
D002945	Cisplatin	Cisplatin affects the expression of RUNX3 mRNA	23300844
D002945	Cisplatin	Cisplatin results in decreased expression of RUNX3 mRNA	20849824\|2759478
D002945	Cisplatin	RUNX3 protein results in increased susceptibility to Cisplatin	15756676
D003633	Dichlorodiphenyl Dichloroethylene	Dichlorodiphenyl Dichloroethylene results in increased activity of RUNX3 protein	27589886
D004052	Diethylnitrosamine	[Diethylnitrosamine co-treated with beta-Naphthoflavone] results in increased expression of RUNX3 mRNA	18164116
D004137	Dinitrochlorobenzene	Dinitrochlorobenzene results in increased expression of RUNX3 mRNA	21893156
D004221	Disulfiram	Disulfiram results in decreased expression of RUNX3 mRNA	20530235
D004317	Doxorubicin	RUNX3 protein results in decreased export of Doxorubicin	15756676
D004317	Doxorubicin	RUNX3 protein results in increased susceptibility to Doxorubicin	15756676
C118739	entinostat	entinostat results in increased expression of RUNX3 mRNA	26272509\|2718838
C118739	entinostat	"[NOG protein co-treated with entinostat co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of RUNX3 mRNA"	27188386
C074283	estradiol 3-benzoate	estradiol 3-benzoate results in increased methylation of RUNX3 promoter	27415467
D004997	Ethinyl Estradiol	Ethinyl Estradiol affects the expression of RUNX3 mRNA	20227414
D005047	Etoposide	RUNX3 protein results in increased susceptibility to Etoposide	15756676
D005419	Flavonoids	Flavonoids results in increased expression of RUNX3 mRNA	18035473
D004397	Fonofos	Fonofos results in increased methylation of RUNX3 promoter	22847954
D005839	Gentamicins	Gentamicins results in decreased expression of RUNX3 mRNA	20849824
D005839	Gentamicins	Gentamicins results in increased expression of RUNX3 mRNA	22061828
C004312	glycidol	glycidol results in increased expression of RUNX3 mRNA	24915197
C561695	(+)-JQ1 compound	(+)-JQ1 compound results in decreased expression of RUNX3 mRNA	23086925\|2479639
D016685	Mitomycin	RUNX3 protein results in increased susceptibility to Mitomycin	15756676
D008942	Mitoxantrone	RUNX3 protein affects the susceptibility to Mitoxantrone	16217747
D009151	Mustard Gas	Mustard Gas results in increased expression of RUNX3 mRNA	15674844
D037742	Nanotubes, Carbon	"Nanotubes, Carbon analog results in increased expression of RUNX3 mRNA"	25554681
D037742	Nanotubes, Carbon	"Nanotubes, Carbon results in increased expression of RUNX3 mRNA"	25554681
D009532	Nickel	Nickel results in increased expression of RUNX3 mRNA	24768652\|2558310
D010081	Oxazolone	Oxazolone results in increased expression of RUNX3 mRNA	21893156
C496932	panobinostat	"[NOG protein co-treated with panobinostat co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of RUNX3 mRNA"	27188386
C496932	panobinostat	panobinostat results in increased expression of RUNX3 mRNA	26272509
D010278	Parathion	Parathion results in increased methylation of RUNX3 promoter	22847954
D010795	Phthalic Acids	Phthalic Acids results in decreased expression of RUNX3 mRNA	21061450
D010795	Phthalic Acids	Phthalic Acids results in increased expression of RUNX3 mRNA	21061450
D012834	Silver	Silver results in decreased expression of RUNX3 mRNA	26551752
D018038	Sodium Selenite	Sodium Selenite results in increased expression of RUNX3 mRNA	18175754
C012568	terbufos	terbufos results in increased methylation of RUNX3 promoter	22847954
D013749	Tetrachlorodibenzodioxin	Tetrachlorodibenzodioxin affects the expression of RUNX3 mRNA	22298810
D013749	Tetrachlorodibenzodioxin	Tetrachlorodibenzodioxin affects the expression of RUNX3 mRNA	24058054
D013749	Tetrachlorodibenzodioxin	Tetrachlorodibenzodioxin promotes the reaction [AHR protein binds to RUNX3 gene]	20819909
D013749	Tetrachlorodibenzodioxin	Tetrachlorodibenzodioxin results in increased expression of RUNX3 mRNA	20819909
D014028	Tobacco Smoke Pollution	Tobacco Smoke Pollution results in decreased expression of RUNX3 mRNA	23724145
D014028	Tobacco Smoke Pollution	Tobacco Smoke Pollution results in decreased methylation of RUNX3 gene	26756918
D014028	Tobacco Smoke Pollution	Tobacco Smoke Pollution results in decreased methylation of RUNX3 promoter	23724145
D014028	Tobacco Smoke Pollution	Tobacco Smoke Pollution results in increased expression of RUNX3 mRNA	28065790
D014212	Tretinoin	Tretinoin results in decreased expression of RUNX3 mRNA	20530235
C015559	trimellitic anhydride	trimellitic anhydride results in increased expression of RUNX3 mRNA	21893156
C016805	tris(1,3-dichloro-2-propyl)phosphate	"tris(1,3-dichloro-2-propyl)phosphate results in decreased expression of RUNX3 mRNA"	26179874
D014635	Valproic Acid	"[NOG protein co-treated with Valproic Acid co-treated with (6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of RUNX3 mRNA"	27188386
D014635	Valproic Acid	Valproic Acid affects the expression of RUNX3 mRNA	25979313
D014635	Valproic Acid	Valproic Acid results in increased expression of RUNX3 mRNA	26272509\|2800136
D014635	Valproic Acid	Valproic Acid results in increased methylation of RUNX3 gene	28853863\|2915479
D014635	Valproic Acid	Valproic Acid affects the expression of RUNX3 mRNA	17292431
D014750	Vincristine	RUNX3 protein results in increased susceptibility to Vincristine	15756676
C029297	vinylidene chloride	vinylidene chloride results in increased expression of RUNX3 mRNA	26682919

GO/Pathway

GO ID	GO Term	Qualifier	Evidence	PubMed
GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	-	ISS	-
GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	-	IBA	21873635
GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	-	ISA	-
GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	-	ISM	19274049
GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	-	ISS	-
GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	-	NAS	19274049
GO:0003700	DNA-binding transcription factor activity	-	TAS	7607690
GO:0005515	protein binding	-	IPI	9751710 17377532 18772112 20100835 20599712 24229708
GO:0005524	ATP binding	-	NAS	7835892

GO ID	GO Term	Qualifier	Evidence	PubMed
GO:0000122	negative regulation of transcription by RNA polymerase II	-	ISS	-
GO:0001503	ossification	-	IBA	21873635
GO:0002062	chondrocyte differentiation	-	IBA	21873635
GO:0006355	regulation of transcription, DNA-templated	-	NAS	7622058
GO:0006357	regulation of transcription by RNA polymerase II	-	IBA	21873635
GO:0006366	transcription by RNA polymerase II	-	TAS	7607690
GO:0006468	protein phosphorylation	-	IDA	20100835
GO:0030097	hemopoiesis	-	IBA	21873635
GO:0030182	neuron differentiation	-	IBA	21873635
GO:0043371	negative regulation of CD4-positive, alpha-beta T cell differentiation	-	ISS	-
GO:0043378	positive regulation of CD8-positive, alpha-beta T cell differentiation	-	ISS	-
GO:0045595	regulation of cell differentiation	-	IBA	21873635
GO:0045786	negative regulation of cell cycle	-	ISS	-
GO:0045893	positive regulation of transcription, DNA-templated	-	IDA	20599712
GO:0048935	peripheral nervous system neuron development	-	TAS	20096094
GO:0050680	negative regulation of epithelial cell proliferation	-	ISS	-
GO:0071559	response to transforming growth factor beta	-	IDA	20599712

GO ID	GO Term	Qualifier	Evidence	PubMed
GO:0000790	nuclear chromatin	-	ISS	-
GO:0005634	nucleus	-	IBA	21873635
GO:0005634	nucleus	-	IDA	20100835 20599712
GO:0005654	nucleoplasm	-	TAS	-
GO:0005730	nucleolus	-	IDA	-
GO:0005737	cytoplasm	-	IDA	20100835 20599712
GO:0005829	cytosol	-	IDA	-
GO:0005829	cytosol	-	TAS	-
GO:0016513	core-binding factor complex	-	TAS	18258917
GO:0043231	intracellular membrane-bounded organelle	-	IDA	-

KEGG ID	KEGG Term

Reactome ID	Reactome Term	Evidence
R-HSA-162582	Signal Transduction	TAS
R-HSA-195721	Signaling by WNT	TAS
R-HSA-201681	TCF dependent signaling in response to WNT	TAS
R-HSA-201722	Formation of the beta-catenin:TCF transactivating complex	TAS
R-HSA-212436	Generic Transcription Pathway	TAS
R-HSA-212436	Generic Transcription Pathway	IEA
R-HSA-4411364	Binding of TCF/LEF:CTNNB1 to target gene promoters	TAS
R-HSA-73857	RNA Polymerase II Transcription	TAS
R-HSA-73857	RNA Polymerase II Transcription	IEA
R-HSA-74160	Gene expression (Transcription)	TAS
R-HSA-74160	Gene expression (Transcription)	IEA
R-HSA-8878159	Transcriptional regulation by RUNX3	TAS
R-HSA-8878159	Transcriptional regulation by RUNX3	IEA
R-HSA-8941855	RUNX3 regulates CDKN1A transcription	TAS
R-HSA-8941856	RUNX3 regulates NOTCH signaling	TAS
R-HSA-8941858	Regulation of RUNX3 expression and activity	TAS
R-HSA-8949275	RUNX3 Regulates Immune Response and Cell Migration	TAS
R-HSA-8949275	RUNX3 Regulates Immune Response and Cell Migration	IEA
R-HSA-8951430	RUNX3 regulates WNT signaling	TAS
R-HSA-8951671	RUNX3 regulates YAP1-mediated transcription	TAS
R-HSA-8951911	RUNX3 regulates RUNX1-mediated transcription	TAS
R-HSA-8951936	RUNX3 regulates p14-ARF	TAS
R-HSA-8952158	RUNX3 regulates BCL2L11 (BIM) transcription	TAS

Interactions (STRING v10.5, Interaction Score >= 0.400)

Publications (Co-occurrence of gene symbol strings and ANCO-Dependence terms)

PMID	Title (Year)	Author	Journal
26756918	Genome-Wide Analysis of DNA Methylation and Cigarette Smoking in a Chinese Population. (2016 Jul)	Zhu X	Environ Health Perspect
26642056	In Utero Cigarette Smoke Affects Allergic Airway Disease But Does Not Alter the Lung Methylome. (2015)	Eyring KR	PLoS One
26203295	Altered placental DNA methylation patterns associated with maternal smoking: current perspectives. (2015 May 7)	Maccani JZ	Adv Genomics Genet
29796116	Genome-wide analysis of DNA methylation in bronchial washings. (2018)	Um SW	Clin Epigenetics
23724145	Long-term exposure to cigarette smoke extract induces hypomethylation at the RUNX3 and IGF2-H19 loci in immortalized human urothelial cells. (2013)	Chen LM	PLoS One
18684727	Genetic variants in RUNX3 and risk of bladder cancer: a haplotype-based analysis. (2008 Oct)	Zhang Z	Carcinogenesis
21380558	Methylation analysis of cancer-related genes in non-neoplastic cells from patients with oral squamous cell carcinoma. (2011 Nov)	de Freitas Cordeiro-Silva M	Mol Biol Rep
12841866	Promoter hypermethylation of tumor suppressor and tumor-related genes in non-small cell lung cancers. (2003 Jul)	Yanagawa N	Cancer Sci
28468586	Alteration in the expression of MGMT and RUNX3 due to non-CpG promoter methylation and their correlation with different risk factors in esophageal cancer patients. (2017 May)	Saikia S	Tumour Biol
18676844	RUNX3 methylation reveals that bladder tumors are older in patients with a history of smoking. (2008 Aug 1)	Wolff EM	Cancer Res
22740873	Application of RUNX3 gene promoter methylation in the diagnosis of non-small cell lung cancer. (2012 Jan)	Yu GP	Oncol Lett
24976992	Association between RUNX3 promoter methylation and non-small cell lung cancer: a meta-analysis. (2014 Jun)	Liang Y	J Thorac Dis
23539450	Genomic aberrations occurring in subsets of serrated colorectal lesions but not conventional adenomas. (2013 May 1)	Burnett-Hartman AN	Cancer Res