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 RXRB

Gene summary

Basic gene Info.	Gene symbol	RXRB
	Gene name	retinoid X receptor, beta
	Synonyms	DAUDI6\|H-2RIIBP\|NR2B2\|RCoR-1
	Cytomap	UCSC genome browser: 6p21.3
	Type of gene	protein-coding
	RefGenes	NM_001270401.1, NM_001291989.1,NM_021976.4,
	Description	MHC class I promoter binding proteinnuclear receptor subfamily 2 group B member 2retinoic acid receptor RXR-beta
	Modification date	20141207
dbXrefs	MIM : 180246
	HGNC : HGNC
	Ensembl : ENSG00000204231
	HPRD : 01578
	Vega : OTTHUMG00000031298
Protein	UniProt: P28702 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RXRB
	BioGPS: 6257
Pathway	NCI Pathway Interaction Database: RXRB
	KEGG: RXRB
	REACTOME: RXRB
	Pathway Commons: RXRB
Context	iHOP: RXRB
	ligand binding site mutation search in PubMed: RXRB
	UCL Cancer Institute: RXRB
Assigned class in mutLBSgeneDB	B: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

GO ID	GO Term	PubMed ID
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	12767074

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Ligand binding site mutations for RXRB

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

LBS	AAchange of nsSNV	Cancer type	# samples
L397	L396P	KIRC	1

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 RXRB

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.

LBS	AAchange of nsSNV	Relative stability change
L397	L396P	-1.0383539

(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 RXRB from PDB

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Differential gene expression and gene-gene network for RXRB

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 RXRB and the right PPI network was created from samples without mutations in the LBS of RXRB. 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 RXRB

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C1458155	Breast Neoplasms	1	Biomarker
umls:C0242656	Disease Progression	1	Biomarker
umls:C0038356	Stomach Neoplasms	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for RXRB

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 status	DrugBank ID	Name	Type	Drug structure
Approved	DB00210	Adapalene	Small molecule
Approved\|investigational	DB00307	Bexarotene	Small molecule
Approved	DB00459	Acitretin	Small molecule
Approved\|investigational	DB00523	Alitretinoin	Small molecule
Approved\|investigational\|nutraceutical	DB00755	Tretinoin	Small molecule
Approved\|investigational	DB00799	Tazarotene	Small molecule
Withdrawn	DB00926	Etretinate	Small molecule
Experimental	DB01941	6-[1-(3,5,5,8,8-Pentamethyl-5,6,7,8-Tetrahydronaphthalen-2-Yl)Cyclopropyl]Pyridine-3-Carboxylic Acid	Small molecule
Experimental	DB07080	N-(2,2,2-TRIFLUOROETHYL)-N-{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL}BENZENESULFONAMIDE	Small molecule
Experimental	DB07929	N-(TERT-BUTYL)-3,5-DIMETHYL-N'-[(5-METHYL-2,3-DIHYDRO-1,4-BENZODIOXIN-6-YL)CARBONYL]BENZOHYDRAZIDE	Small molecule
Experimental	DB08175	(2E,4E)-11-METHOXY-3,7,11-TRIMETHYLDODECA-2,4-DIENOIC ACID	Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of RXRB go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
LG2		LG100268	1h9u	A	L397
LG2		LG100268	1h9u	B	L397
LG2		LG100268	1h9u	C	L397
LG2		LG100268	1h9u	D	L397

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Conservation information for LBS of RXRB

Multiple alignments for P28702 in multiple species

LBS	AA sequence	# species	Species
A342	TNICQAADKQL	3	Homo sapiens, Danio rerio, Danio rerio
A343	NICQAADKQLF	3	Homo sapiens, Danio rerio, Danio rerio
A398	DGILLATGLHV	2	Homo sapiens, Danio rerio
A398	DEILLATGLHV	1	Danio rerio
C503	SIGLKCLEHLF	3	Homo sapiens, Danio rerio, Danio rerio
E524	DTFLMEMLEAP	2	Homo sapiens, Danio rerio
E524	DTFLMEMLESP	1	Danio rerio
F384	LLIASFSHRSI	2	Homo sapiens, Danio rerio
F384	LLIAAFSHRSI	1	Danio rerio
F521	TPIDTFLMEML	3	Homo sapiens, Danio rerio, Danio rerio
H506	LKCLEHLFFFK	3	Homo sapiens, Danio rerio, Danio rerio
I339	DPVTNICQAAD	3	Homo sapiens, Danio rerio, Danio rerio
I381	WNELLIASFSH	2	Homo sapiens, Danio rerio
I381	WNELLIAAFSH	1	Danio rerio
I416	--VGAIFDRVL	1	Homo sapiens
I416	AEVGAIFDRVL	1	Danio rerio
I416	AEVGALFDRVL	1	Danio rerio
K355	LVEWAKRIPHF	2	Homo sapiens, Danio rerio
K355	LVEWAKRVPHF	1	Danio rerio
L365	FSSLPLDDQVI	1	Homo sapiens
L365	FSELSLDDQVI	1	Danio rerio
L365	FSDVPLDDQVI	1	Danio rerio
L372	DQVILLRAGWN	3	Homo sapiens, Danio rerio, Danio rerio
L380	GWNELLIASFS	2	Homo sapiens, Danio rerio
L380	GWNELLIAAFS	1	Danio rerio
L397	RDGILLATGLH	1	Homo sapiens
L397	KDGILLATGLH	1	Danio rerio
L397	KDEILLATGLH	1	Danio rerio
L507	KCLEHLFFFKL	3	Homo sapiens, Danio rerio, Danio rerio
Q346	QAADKQLFTLV	3	Homo sapiens, Danio rerio, Danio rerio
Q368	LPLDDQVILLR	1	Homo sapiens
Q368	LSLDDQVILLR	1	Danio rerio
Q368	VPLDDQVILLR	1	Danio rerio
R373	QVILLRAGWNE	3	Homo sapiens, Danio rerio, Danio rerio
R387	ASFSHRSIDVR	1	Homo sapiens
R387	ASFSHRSITVK	1	Danio rerio
R387	AAFSHRSISVK	1	Danio rerio
T520	DTPIDTFLMEM	2	Homo sapiens, Danio rerio
T520	NTPIDTFLMEM	1	Danio rerio
V351	QLFTLVEWAKR	3	Homo sapiens, Danio rerio, Danio rerio
V369	PLDDQVILLRA	2	Homo sapiens, Danio rerio
V369	SLDDQVILLRA	1	Danio rerio
V413	-----VGAIFD	1	Homo sapiens
V413	AHNAEVGAIFD	1	Danio rerio
V413	SHSAEVGALFD	1	Danio rerio
W376	LLRAGWNELLI	3	Homo sapiens, Danio rerio, Danio rerio