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 RARB
Gene summary
Basic gene Info.Gene symbolRARB
Gene nameretinoic acid receptor, beta
SynonymsHAP|MCOPS12|NR1B2|RRB2
CytomapUCSC genome browser: 3p24.2
Type of geneprotein-coding
RefGenesNM_000965.4,
NM_001290216.1,NM_001290217.1,NM_001290266.1,NM_001290276.1,
NM_001290277.1,NM_001290300.1,NM_016152.3,NR_110892.1,
NR_110893.1,
DescriptionHBV-activated proteinRAR-betaRAR-epsilonhepatitis B virus activated proteinnuclear receptor subfamily 1 group B member 2retinoic acid receptor betaretinoic acid receptor, beta polypeptide
Modification date20141207
dbXrefs MIM : 180220
HGNC : HGNC
Ensembl : ENSG00000077092
HPRD : 07183
Vega : OTTHUMG00000130480
ProteinUniProt: P10826
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RARB
BioGPS: 5915
PathwayNCI Pathway Interaction Database: RARB
KEGG: RARB
REACTOME: RARB
Pathway Commons: RARB
ContextiHOP: RARB
ligand binding site mutation search in PubMed: RARB
UCL Cancer Institute: RARB
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


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Ligand binding site mutations for RARB
Lollipop-style diagram of mutations at LBS in amino-acid sequence.
We represented ligand binding site mutations only. (You can see big image via clicking.)
 
: non-synonymous mutation on LBS, Circle size denotes number of samples.

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
D127K128NBLCA1
L409L409VBLCA1
R276T278ACOAD1
C140Q141ECOAD1
E62T63ACOAD1
I270L271RHNSC1
P408P408HLUAD1
R394R394PSTAD1
F249T250ASTAD1
C143Y142SSTAD1
I254A255TSTAD1
C140R139QUCEC1
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 RARB
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
I254A255T-1.4805283
D127K128N-1.3523154
E62T63A-1.3507575
C140Q141E-1.3198812
I270L271R-1.3138079
C140R139Q-1.2275885
R276T278A-1.1160216
L409L409V-0.96258638
P408P408H-0.92037283
R394R394P-0.77466933
C143Y142S-0.6667526
F249T250A-0.23057925
(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 RARB from PDB

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Differential gene expression and gene-gene network for RARB
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 RARB and the right PPI network was created from samples without mutations in the LBS of RARB. 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 RARB
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0007137Carcinoma, Squamous Cell13AlteredExpression, Biomarker, PostTranslationalModification
umls:C1458155Breast Neoplasms8AlteredExpression, Biomarker, PostTranslationalModification, Therapeutic
umls:C0024121Lung Neoplasms6AlteredExpression, Biomarker
umls:C0018671Head and Neck Neoplasms2Biomarker
umls:C0001418Adenocarcinoma2Biomarker
umls:C0038356Stomach Neoplasms2Biomarker
umls:C3809803MICROPHTHALMIA, SYNDROMIC 121GeneticVariation
umls:C0014175Endometriosis1Biomarker
umls:C0149940Sciatic Neuropathy1Biomarker
umls:C0007873Uterine Cervical Neoplasms1Biomarker

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

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Pharmacological information for RARB
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.

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
ApprovedDB00210AdapaleneSmall molecule
ApprovedDB00459AcitretinSmall molecule
Approved|investigationalDB00523AlitretinoinSmall molecule
Approved|investigationalDB00799TazaroteneSmall molecule
WithdrawnDB00926EtretinateSmall molecule
ExperimentalDB02877TTNPBSmall molecule
Approved|investigationalDB04942TamibaroteneSmall molecule
InvestigationalDB05785LGD-1550Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of RARB go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS


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Conservation information for LBS of RARB
Multiple alignments for P10826 in multiple species
LBSAA sequence# speciesSpecies
A232KFSELATKCII3Homo sapiens, Gallus gallus, Mus musculus
A232KFSELSTKCII1Danio rerio
C124NMIYTCHRDKN2Homo sapiens, Mus musculus
C124NMVYTCHRDKN2Danio rerio, Gallus gallus
C130HRDKNCVINKV3Homo sapiens, Gallus gallus, Mus musculus
C130HRDKNCQINKV1Danio rerio
C140VTRNRCQYCRL4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
C143NRCQYCRLQKC4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
C235ELATKCIIKIV3Homo sapiens, Gallus gallus, Mus musculus
C235ELSTKCIIKIV1Danio rerio
D127YTCHRDKNCVI3Homo sapiens, Gallus gallus, Mus musculus
D127YTCHRDKNCQI1Danio rerio
E412PPLIQEMLENS3Homo sapiens, Gallus gallus, Mus musculus
E412PPLIREMLENP1Danio rerio
E415IQEMLENSEGH3Homo sapiens, Gallus gallus, Mus musculus
E415IREMLENPEAF1Danio rerio
E62----VETQSTS2Danio rerio, Gallus gallus
E62----IETQSTS1Homo sapiens
E62LNAAIETQSTS1Mus musculus
F199AHQETFPSLCQ4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
F228GLWDKFSELAT3Homo sapiens, Gallus gallus, Mus musculus
F228GLWDKFSELST1Danio rerio
F249KRLPGFTGLTI2Homo sapiens, Mus musculus
F249KRLPGFTTLTI1Danio rerio
F249KRLPGFTSLTI1Gallus gallus
F286QDTMTFSDGLT4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
F302MHNAGFGPLTD4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
G301QMHNAGFGPLT4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
G391SISAKGAERVI3Homo sapiens, Gallus gallus, Mus musculus
G391GISTKGAERAI1Danio rerio
I254FTGLTIADQIT2Homo sapiens, Mus musculus
I254FTTLTIADQIT1Danio rerio
I254FTSLTIADQIT1Gallus gallus
I258TIADQITLLKA3Homo sapiens, Gallus gallus, Mus musculus
I258TIADQITLLKS1Danio rerio
I270CLDILILRICT3Homo sapiens, Gallus gallus, Mus musculus
I270CLDILMLRICT1Danio rerio
I273ILILRICTRYT3Homo sapiens, Gallus gallus, Mus musculus
I273ILMLRICTRYT1Danio rerio
I410SMPPLIQEMLE3Homo sapiens, Gallus gallus, Mus musculus
I410PMPPLIREMLE1Danio rerio
K244IVEFAKRLPGF4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
K262QITLLKAACLD3Homo sapiens, Gallus gallus, Mus musculus
K262QITLLKSACLD1Danio rerio
L231DKFSELATKCI3Homo sapiens, Gallus gallus, Mus musculus
L231DKFSELSTKCI1Danio rerio
L261DQITLLKAACL3Homo sapiens, Gallus gallus, Mus musculus
L261DQITLLKSACL1Danio rerio
L266LKAACLDILIL3Homo sapiens, Gallus gallus, Mus musculus
L266LKSACLDILML1Danio rerio
L269ACLDILILRIC3Homo sapiens, Gallus gallus, Mus musculus
L269ACLDILMLRIC1Danio rerio
L305AGFGPLTDLVF4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
L319NQLLPLEMDDT3Homo sapiens, Gallus gallus, Mus musculus
L319GQLLPLEMDDT1Danio rerio
L398ERVITLKMEIP3Homo sapiens, Gallus gallus, Mus musculus
L398ERAITLKMEIP1Danio rerio
L409GSMPPLIQEML3Homo sapiens, Gallus gallus, Mus musculus
L409GPMPPLIREML1Danio rerio
L414LIQEMLENSEG3Homo sapiens, Gallus gallus, Mus musculus
L414LIREMLENPEA1Danio rerio
M413PLIQEMLENSE3Homo sapiens, Gallus gallus, Mus musculus
M413PLIREMLENPE1Danio rerio
P408PGSMPPLIQEM3Homo sapiens, Gallus gallus, Mus musculus
P408PGPMPPLIREM1Danio rerio
Q257LTIADQITLLK4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
Q411MPPLIQEMLEN3Homo sapiens, Gallus gallus, Mus musculus
Q411MPPLIREMLEN1Danio rerio
R126IYTCHRDKNCV2Homo sapiens, Mus musculus
R126VYTCHRDKNCQ1Danio rerio
R126VYTCHRDKNCV1Gallus gallus
R276LRICTRYTPEQ4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
R394AKGAERVITLK3Homo sapiens, Gallus gallus, Mus musculus
R394TKGAERAITLK1Danio rerio
S287DTMTFSDGLTL4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
V240CIIKIVEFAKR4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus
V309PLTDLVFTFAN3Homo sapiens, Gallus gallus, Mus musculus
V309PLTDLVFAFAG1Danio rerio
V395KGAERVITLKM3Homo sapiens, Gallus gallus, Mus musculus
V395KGAERAITLKM1Danio rerio
W225LDLGLWDKFSE4Homo sapiens, Danio rerio, Gallus gallus, Mus musculus


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