Gene info: ID 4004

Gene: LMO1

GENE ID: 4004

Synonyms: RBTN1|RHOM1|TTG1

Description: LIM domain only 1

Gene type: protein-coding

Location: 11p15.4

dbXrefs: Ensembl:ENSG00000166407 MIM:186921 Vega:OTTHUMG00000165833 UniprotKB:P25800

RefSeq: NG_032827.2

Retrived from: PubMed|SNP Mapped

SNPs: 7 ANCO-SNPs

Phenotype: AD

# Publications: 1

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

Pascal p-value : 7.028e-1 (AD) 1.891e-1 (ND)

ANCO-SNPs

SNP ID	Position	Alleles	Trait	Variation Type
rs204926	chr11:8233559 (GRCh38.p7)	G>A	alcohol dependence	SNV(Single Nucleotide Variation)
rs12574271	chr11:8232956 (GRCh38.p7)	G>T	alcohol dependence	SNV(Single Nucleotide Variation)
rs110420	chr11:8231502 (GRCh38.p7)	T>C	alcohol dependence	SNV(Single Nucleotide Variation)
rs11041820	chr11:8229891 (GRCh38.p7)	G>A	alcohol dependence	SNV(Single Nucleotide Variation)
rs4758317	chr11:8229264 (GRCh38.p7)	C>A	alcohol dependence	SNV(Single Nucleotide Variation)
rs2290450	chr11:8226935 (GRCh38.p7)	C>T	alcohol dependence	SNV(Single Nucleotide Variation)
rs2290451	chr11:8226893 (GRCh38.p7)	C>A / C>G	alcohol dependence	SNV(Single Nucleotide Variation)

DNA Methylation

Probe	Locus(GRCh37)	Gene	Region	p-val	Trait	PubMed ID
cg23162201	chr11:8280741	LMO1		7.200e-9	Smoking	27651444

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
HS3ST2	0.712
EFHD2	0.661
F12	0.632
RPRM	0.625
IFITM10	0.611
EBP	0.602
LRMP	0.594
HS3ST4	0.593
SLC35F1	0.591
THOC6	0.586

Top 10 negatively co-expressed genes

Gene Symbol	Pearson Correlation Coefficient
MRO	-0.417
ANGPTL1	-0.411
RXRG	-0.409
ASB4	-0.386
HKDC1	-0.383
EYA1	-0.381
PARD3B	-0.374
PPARA	-0.37
ACBD7	-0.365
PARD3	-0.362

There is no DrugBank record for this gene !

ID	Drug Name	Action	PubMed
C459179	4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	"[NOG protein co-treated with mercuric bromide 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 decreased expression of LMO1 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 p-Chloromercuribenzoic 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 decreased expression of LMO1 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 Phenylmercuric Acetate 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 decreased expression of LMO1 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 decreased expression of LMO1 mRNA"	27188386
C516138	(6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine	"[NOG protein co-treated with mercuric bromide 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 decreased expression of LMO1 mRNA"	27188386
C516138	(6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine	"[NOG protein co-treated with p-Chloromercuribenzoic 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 decreased expression of LMO1 mRNA"	27188386
C516138	(6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine	"[NOG protein co-treated with Phenylmercuric Acetate 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 decreased expression of LMO1 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 decreased expression of LMO1 mRNA"	27188386
D000082	Acetaminophen	Acetaminophen results in decreased expression of LMO1 mRNA	26690555
D016604	Aflatoxin B1	Aflatoxin B1 results in increased expression of LMO1 mRNA	22100608
D016604	Aflatoxin B1	Aflatoxin B1 results in increased methylation of LMO1 gene	28458013
D000452	Aldrin	Aldrin results in increased expression of LMO1 mRNA	18579281
D000643	Ammonium Chloride	Ammonium Chloride affects the expression of LMO1 mRNA	16483693
D001554	Benzene	Benzene results in increased expression of LMO1 mRNA	15120971\|1512265
C006780	bisphenol A	bisphenol A affects the methylation of LMO1 promoter	27334623
C006780	bisphenol A	bisphenol A results in decreased expression of LMO1 mRNA	25181051
D002220	Carbamazepine	Carbamazepine affects the expression of LMO1 mRNA	25979313
D020245	p-Chloromercuribenzoic Acid	"[NOG protein co-treated with p-Chloromercuribenzoic 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 decreased expression of LMO1 mRNA"	27188386
D020245	p-Chloromercuribenzoic Acid	p-Chloromercuribenzoic Acid results in decreased expression of LMO1 mRNA	26272509
D002794	Choline	[Methionine deficiency co-treated with Choline deficiency co-treated with Folic Acid deficiency] results in increased methylation of LMO1 gene	20938992
D003471	Cuprizone	Cuprizone results in decreased expression of LMO1 mRNA	26577399
C016366	dibenzothiophene	dibenzothiophene results in decreased expression of LMO1 mRNA	23656968
D002945	Cisplatin	Cisplatin promotes the reaction [jinfukang results in decreased expression of LMO1 mRNA]	27392435
D002945	Cisplatin	Cisplatin results in decreased expression of LMO1 mRNA	27392435
D002945	Cisplatin	jinfukang promotes the reaction [Cisplatin results in decreased expression of LMO1 mRNA]	27392435
D004026	Dieldrin	Dieldrin results in increased expression of LMO1 mRNA	20438755
D004041	Dietary Fats	Dietary Fats results in increased expression of LMO1 mRNA	18042831\|1903023
D004041	Dietary Fats	rimonabant inhibits the reaction [Dietary Fats results in increased expression of LMO1 mRNA]	19030233
D005419	Flavonoids	Flavonoids results in decreased expression of LMO1 mRNA	18035473
D005492	Folic Acid	[Methionine deficiency co-treated with Choline deficiency co-treated with Folic Acid deficiency] results in increased methylation of LMO1 gene	20938992
C039281	furan	furan results in increased expression of LMO1 mRNA	27387713
D017313	Fenretinide	Fenretinide results in decreased expression of LMO1 mRNA	28973697
C544151	jinfukang	Cisplatin promotes the reaction [jinfukang results in decreased expression of LMO1 mRNA]	27392435
C544151	jinfukang	jinfukang promotes the reaction [Cisplatin results in decreased expression of LMO1 mRNA]	27392435
C561695	(+)-JQ1 compound	(+)-JQ1 compound results in decreased expression of LMO1 mRNA	25961927
D007608	Kainic Acid	Kainic Acid results in decreased expression of LMO1 mRNA	17997037
C042720	mercuric bromide	mercuric bromide results in decreased expression of LMO1 mRNA	26272509
C042720	mercuric bromide	"[NOG protein co-treated with mercuric bromide 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 decreased expression of LMO1 mRNA"	27188386
D008715	Methionine	[Methionine deficiency co-treated with Choline deficiency co-treated with Folic Acid deficiency] results in increased methylation of LMO1 gene	20938992
D008727	Methotrexate	Methotrexate affects the expression of LMO1 mRNA	18502557
C004925	methylmercuric chloride	methylmercuric chloride results in decreased expression of LMO1 mRNA	28001369
D037742	Nanotubes, Carbon	"Nanotubes, Carbon analog results in increased expression of LMO1 mRNA"	25554681
C028007	nickel monoxide	nickel monoxide results in decreased expression of LMO1 mRNA	19167457
D000073878	Palm Oil	Palm Oil results in increased expression of LMO1 mRNA	18042831
D010662	Phenylmercuric Acetate	"[NOG protein co-treated with Phenylmercuric Acetate 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 decreased expression of LMO1 mRNA"	27188386
D010662	Phenylmercuric Acetate	Phenylmercuric Acetate results in decreased expression of LMO1 mRNA	26272509
C006253	pirinixic acid	pirinixic acid results in increased expression of LMO1 mRNA	20813756
D010936	Plant Extracts	Plant Extracts results in decreased expression of LMO1 mRNA	23557933
C089032	rimonabant	rimonabant inhibits the reaction [Dietary Fats results in increased expression of LMO1 mRNA]	19030233
C017947	sodium arsenite	sodium arsenite results in increased expression of LMO1 mRNA	16356559
D013893	Thiram	Thiram results in increased expression of LMO1 mRNA	20530235
D014212	Tretinoin	Tretinoin results in decreased expression of LMO1 mRNA	20530235
D014212	Tretinoin	Tretinoin results in decreased expression of LMO1 mRNA	23724009\|2383079
C012589	trichostatin A	trichostatin A results in decreased expression of LMO1 mRNA	24935251
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 decreased expression of LMO1 mRNA"	27188386
D014635	Valproic Acid	Valproic Acid affects the expression of LMO1 mRNA	25979313
D014635	Valproic Acid	Valproic Acid results in decreased expression of LMO1 mRNA	24383497\|2627250
D014635	Valproic Acid	Valproic Acid affects the expression of LMO1 mRNA	17292431
D014635	Valproic Acid	Valproic Acid results in decreased expression of LMO1 mRNA	24896083
D001335	Vehicle Emissions	Vehicle Emissions results in decreased methylation of LMO1 gene	25560391
C111237	vorinostat	vorinostat results in decreased expression of LMO1 mRNA	27188386

GO/Pathway

GO ID	GO Term	Qualifier	Evidence	PubMed
GO:0005515	protein binding	-	IPI	21516116 25416956 27107012
GO:0046872	metal ion binding	-	IEA	-

GO ID	GO Term	Qualifier	Evidence	PubMed
GO:0000122	negative regulation of transcription by RNA polymerase II	-	IEA	-
GO:0045944	positive regulation of transcription by RNA polymerase II	-	IMP	20855495
GO:0046013	regulation of T cell homeostatic proliferation	-	IEA	-
GO:1902036	regulation of hematopoietic stem cell differentiation	-	TAS	-

GO ID	GO Term	Qualifier	Evidence	PubMed
GO:0005634	nucleus	-	ISS	-
GO:0005654	nucleoplasm	-	TAS	-

KEGG ID	KEGG Term

Reactome ID	Reactome Term	Evidence
R-HSA-212436	Generic Transcription Pathway	TAS
R-HSA-73857	RNA Polymerase II Transcription	TAS
R-HSA-74160	Gene expression (Transcription)	TAS
R-HSA-8878171	Transcriptional regulation by RUNX1	TAS
R-HSA-8939236	RUNX1 regulates transcription of genes involved in differentiation of HSCs	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
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks. (2013 Oct)	Kapoor M	Hum Genet