mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for LMO2
Gene summary
Basic gene Info.Gene symbolLMO2
Gene nameLIM domain only 2 (rhombotin-like 1)
SynonymsRBTN2|RBTNL1|RHOM2|TTG2
CytomapUCSC genome browser: 11p13
Type of geneprotein-coding
RefGenesNM_001142315.1,
NM_001142316.1,NM_005574.3,
DescriptionLIM domain only protein 2LMO-2T-cell translocation gene 2T-cell translocation protein 2cysteine-rich protein TTG-2rhombotin 2rhombotin-2rhombotin-like 1
Modification date20141207
dbXrefs MIM : 180385
HGNC : HGNC
Ensembl : ENSG00000135363
HPRD : 01586
Vega : OTTHUMG00000157176
ProteinUniProt: P25791
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LMO2
BioGPS: 4005
PathwayNCI Pathway Interaction Database: LMO2
KEGG: LMO2
REACTOME: LMO2
Pathway Commons: LMO2
ContextiHOP: LMO2
ligand binding site mutation search in PubMed: LMO2
UCL Cancer Institute: LMO2
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0042789mRNA transcription from RNA polymerase II promoter16314316
GO:0045944positive regulation of transcription from RNA polymerase II promoter16314316
GO:0097067cellular response to thyroid hormone stimulus19375645


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Ligand binding site mutations for LMO2

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
R81R81WBRCA1
E145E145KCOAD1
C125Q126ELUAD1
R40R40SLUAD1
G132G132ALUAD1
R69R69LLUSC1
D147D147NSKCM1
R102R102CSKCM1
C125A124VSKCM1
E145E145KSKCM1
R102R102HSTAD1
C130C130RSTAD1
R81R81LSTAD1
E105E105DUCEC1
I101I101MUCEC1
C33Q35HUCEC1
G132G132CUCEC1
cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma.


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Protein structure related information for LMO2
Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
  (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)
: nsSNV at non-LBS: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.
LBSAAchange of nsSNVRelative stability change
C130C130R-1.2825234
R40R40S-1.1377328
R102R102H-1.0546466
R81R81W-0.92136437
I101I101M-0.87440781
R102R102C-0.79622962
E105E105D-0.73240148
E145E145K-0.66684043
R81R81L-0.6480299
D147D147N-0.6444738
C33Q35H-0.61341812
C125A124V-0.54450124
G132G132A-0.4997136
G132G132C-0.26120474
C125Q126E-0.076074925
R69R69L-0.009839719
(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for LMO2 from PDB

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Differential gene expression and gene-gene network for LMO2
Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)
* Left PPI network was created from samples with mutations in the LBS of LMO2 and the right PPI network was created from samples without mutations in the LBS of LMO2. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


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Phenotype information for LMO2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C1961099Precursor T-Cell Lymphoblastic Leukemia-Lymphoma22Biomarker, GeneticVariation
umls:C0023492Leukemia, T-Cell9Biomarker

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

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Pharmacological information for LMO2
Gene expression profile of anticancer drug treated cell-lines (CCLE)
Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of LMO2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ZNZINC(2+)2xjyAC125 D147
ZNZINC(2+)2ypaCC125 D147
ZNZINC(2+)4kfzAC125 D147
ZNZINC(2+)4kfzBC125 D147
ZNZINC(2+)2xjyAC33
ZNZINC(2+)2ypaCC33
ZNZINC(2+)4kfzAC33
ZNZINC(2+)4kfzBC33
IIIPeptide ligand (ASP,VAL,MET,VAL,VAL,GLY,GLU,PRO,THR,LEU,MET,GLY,GLY,GLU,PHE,GLY,ASP,GLU,ASP,GLU,ARG,LEU,ILE,THR,ARG,LEU,GLU,ASN,THR)2xjzAR102
IIIPeptide ligand (ASP,VAL,MET,VAL,VAL,GLY,GLU,PRO,THR,LEU,MET,GLY,GLY,GLU,PHE,GLY,ASP,GLU,ASP,GLU,ARG)2xjzCR102
IIIPeptide ligand (ASP,VAL,MET,VAL,VAL,GLY,GLU,PRO,THR,LEU,MET,GLY,GLY,GLU,PHE,GLY,ASP,GLU,ASP,GLU,ARG,LEU,ILE,THR,ARG,LEU,GLU,ASN,THR)2xjzDR102
IIIPeptide ligand (ASP,VAL,MET,VAL,VAL,GLY,GLU,PRO,THR,LEU,MET,GLY,GLY,GLU,PHE,GLY,ASP,GLU,ASP,GLU,ARG,LEU,ILE,THR,ARG,LEU)2xjzER102


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Conservation information for LBS of LMO2
Multiple alignments for P25791 in multiple species
LBSAA sequence# speciesSpecies
A103DKRIRAYEMTM1Homo sapiens
A103EKRIRAFEMTM1Danio rerio
A103DKRIRAFEMTM1Xenopus tropicalis
C122LECFKCAACQK3Homo sapiens, Danio rerio, Xenopus tropicalis
C125FKCAACQKHFC3Homo sapiens, Danio rerio, Xenopus tropicalis
C130CQKHFCVGDRY3Homo sapiens, Danio rerio, Xenopus tropicalis
C144NSDIVCEQDIY2Homo sapiens, Xenopus tropicalis
C144NSDIVCEQDIF1Danio rerio
C30PSLLTCGGCQQ3Homo sapiens, Danio rerio, Xenopus tropicalis
C33LTCGGCQQSIG2Danio rerio, Xenopus tropicalis
C33LTCGGCQQNIG1Homo sapiens
C54YWHEDCLSCDL3Homo sapiens, Danio rerio, Xenopus tropicalis
C57EDCLSCDLCGC3Homo sapiens, Danio rerio, Xenopus tropicalis
C60LSCDLCGCRLG3Homo sapiens, Danio rerio, Xenopus tropicalis
C80LGRKLCRRDYL3Homo sapiens, Danio rerio, Xenopus tropicalis
D133HFCVGDRYLLI3Homo sapiens, Danio rerio, Xenopus tropicalis
D147IVCEQDIYEWT2Homo sapiens, Xenopus tropicalis
D147IVCEQDIFEWT1Danio rerio
D39QQNIGDRYFLK1Homo sapiens
D39QQSIGDRFFLK1Danio rerio
D39QQSIGDRYFLK1Xenopus tropicalis
D83KLCRRDYLRLF3Homo sapiens, Danio rerio, Xenopus tropicalis
D91RLFGQDGLCAS3Homo sapiens, Danio rerio, Xenopus tropicalis
E105RIRAFEMTMRV2Danio rerio, Xenopus tropicalis
E105RIRAYEMTMRV1Homo sapiens
E145SDIVCEQDIYE2Homo sapiens, Xenopus tropicalis
E145SDIVCEQDIFE1Danio rerio
E52DQYWHEDCLSC2Homo sapiens, Xenopus tropicalis
E52EQYWHEDCLSC1Danio rerio
F120YHLECFKCAAC3Homo sapiens, Danio rerio, Xenopus tropicalis
F129ACQKHFCVGDR3Homo sapiens, Danio rerio, Xenopus tropicalis
F42IGDRYFLKAID2Homo sapiens, Xenopus tropicalis
F42IGDRFFLKAIE1Danio rerio
G132KHFCVGDRYLL3Homo sapiens, Danio rerio, Xenopus tropicalis
G92LFGQDGLCASC3Homo sapiens, Danio rerio, Xenopus tropicalis
H51IDQYWHEDCLS2Homo sapiens, Xenopus tropicalis
H51IEQYWHEDCLS1Danio rerio
I101SCDKRIRAYEM1Homo sapiens
I101SCEKRIRAFEM1Danio rerio
I101SCDKRIRAFEM1Xenopus tropicalis
I46YFLKAIDQYWH2Homo sapiens, Xenopus tropicalis
I46FFLKAIEQYWH1Danio rerio
K111MTMRVKDKVYH2Homo sapiens, Xenopus tropicalis
K111MTMRVRDKVYH1Danio rerio
K44DRYFLKAIDQY2Homo sapiens, Xenopus tropicalis
K44DRFFLKAIEQY1Danio rerio
K74RRLYYKLGRKL3Homo sapiens, Danio rerio, Xenopus tropicalis
L117DKVYHLECFKC3Homo sapiens, Danio rerio, Xenopus tropicalis
L136VGDRYLLINSD3Homo sapiens, Danio rerio, Xenopus tropicalis
L137GDRYLLINSDI3Homo sapiens, Danio rerio, Xenopus tropicalis
L43GDRYFLKAIDQ2Homo sapiens, Xenopus tropicalis
L43GDRFFLKAIEQ1Danio rerio
L55WHEDCLSCDLC3Homo sapiens, Danio rerio, Xenopus tropicalis
L64LCGCRLGEVGR3Homo sapiens, Danio rerio, Xenopus tropicalis
L71EVGRRLYYKLG3Homo sapiens, Danio rerio, Xenopus tropicalis
L85CRRDYLRLFGQ3Homo sapiens, Danio rerio, Xenopus tropicalis
M106IRAYEMTMRVK1Homo sapiens
M106IRAFEMTMRVR1Danio rerio
M106IRAFEMTMRVK1Xenopus tropicalis
M108AYEMTMRVKDK1Homo sapiens
M108AFEMTMRVRDK1Danio rerio
M108AFEMTMRVKDK1Xenopus tropicalis
Q146DIVCEQDIYEW2Homo sapiens, Xenopus tropicalis
Q146DIVCEQDIFEW1Danio rerio
Q90LRLFGQDGLCA3Homo sapiens, Danio rerio, Xenopus tropicalis
R102CDKRIRAYEMT1Homo sapiens
R102CEKRIRAFEMT1Danio rerio
R102CDKRIRAFEMT1Xenopus tropicalis
R109YEMTMRVKDKV1Homo sapiens
R109FEMTMRVRDKV1Danio rerio
R109FEMTMRVKDKV1Xenopus tropicalis
R134FCVGDRYLLIN3Homo sapiens, Danio rerio, Xenopus tropicalis
R40QNIGDRYFLKA1Homo sapiens
R40QSIGDRFFLKA1Danio rerio
R40QSIGDRYFLKA1Xenopus tropicalis
R69LGEVGRRLYYK3Homo sapiens, Danio rerio, Xenopus tropicalis
R70GEVGRRLYYKL3Homo sapiens, Danio rerio, Xenopus tropicalis
R81GRKLCRRDYLR3Homo sapiens, Danio rerio, Xenopus tropicalis
T107RAYEMTMRVKD1Homo sapiens
T107RAFEMTMRVRD1Danio rerio
T107RAFEMTMRVKD1Xenopus tropicalis
V110EMTMRVKDKVY2Homo sapiens, Xenopus tropicalis
V110EMTMRVRDKVY1Danio rerio
V114RVKDKVYHLEC2Homo sapiens, Xenopus tropicalis
V114RVRDKVYHLEC1Danio rerio
V131QKHFCVGDRYL3Homo sapiens, Danio rerio, Xenopus tropicalis
Y104KRIRAFEMTMR2Danio rerio, Xenopus tropicalis
Y104KRIRAYEMTMR1Homo sapiens
Y135CVGDRYLLINS3Homo sapiens, Danio rerio, Xenopus tropicalis
Y41NIGDRYFLKAI1Homo sapiens
Y41SIGDRFFLKAI1Danio rerio
Y41SIGDRYFLKAI1Xenopus tropicalis
Y72VGRRLYYKLGR3Homo sapiens, Danio rerio, Xenopus tropicalis
Y73GRRLYYKLGRK3Homo sapiens, Danio rerio, Xenopus tropicalis
Y84LCRRDYLRLFG3Homo sapiens, Danio rerio, Xenopus tropicalis


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