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 XPA
Gene summary
Basic gene Info.Gene symbolXPA
Gene namexeroderma pigmentosum, complementation group A
CytomapUCSC genome browser: 9q22.3
Type of geneprotein-coding
DescriptionDNA repair protein complementing XP-A cellsexcision repair-controllingmutant xeroderma pigmentosum complementation group Axeroderma pigmentosum group A-complementing protein
Modification date20141222
dbXrefs MIM : 611153
Ensembl : ENSG00000136936
HPRD : 02045
Vega : OTTHUMG00000020330
ProteinUniProt: P23025
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_XPA
BioGPS: 7507
PathwayNCI Pathway Interaction Database: XPA
Pathway Commons: XPA
ContextiHOP: XPA
ligand binding site mutation search in PubMed: XPA
UCL Cancer Institute: XPA
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

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

Ligand binding site mutations for XPA
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
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.

Protein structure related information for XPA
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
(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 XPA from PDB

Differential gene expression and gene-gene network for XPA
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 XPA and the right PPI network was created from samples without mutations in the LBS of XPA. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for XPA
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0043346Xeroderma Pigmentosum30Biomarker, GeneticVariation
umls:C1337030XPA GENE4GeneticVariation
umls:C0037286Skin Neoplasms4Biomarker, GeneticVariation
umls:C0007117Carcinoma, Basal Cell2Biomarker, GeneticVariation
umls:C0021841Intestinal Neoplasms1Biomarker
umls:C1449861Micronuclei, Chromosome-Defective1Biomarker

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

Pharmacological information for XPA
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 XPA go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of XPA
Multiple alignments for P23025 in multiple species
LBSAA sequence# speciesSpecies
C105FDYVICEECGK1Homo sapiens
C105VQYEECLECGD1Drosophila melanogaster
C105FDYTICEECGK1Mus musculus
C108VICEECGKEFM1Homo sapiens
C108EECLECGDMFA1Drosophila melanogaster
C108TICEECGKEFM1Mus musculus
C129PTCDNCRDADD1Homo sapiens
C129SVCDKCRDKDE1Drosophila melanogaster
C129PTCDSCRDADD1Mus musculus

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