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 PTP4A1
Gene summary
Basic gene Info.Gene symbolPTP4A1
Gene nameprotein tyrosine phosphatase type IVA, member 1
CytomapUCSC genome browser: 6q12
Type of geneprotein-coding
Descriptionprotein tyrosine phosphatase type IVA 1protein tyrosine phosphatase type IVA protein 1protein-tyrosine phosphatase 4a1protein-tyrosine phosphatase of regenerating liver 1
Modification date20141207
dbXrefs MIM : 601585
Ensembl : ENSG00000112245
HPRD : 03349
Vega : OTTHUMG00000014949
ProteinUniProt: Q93096
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PTP4A1
BioGPS: 7803
PathwayNCI Pathway Interaction Database: PTP4A1
Pathway Commons: PTP4A1
ContextiHOP: PTP4A1
ligand binding site mutation search in PubMed: PTP4A1
UCL Cancer Institute: PTP4A1
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 PTP4A1

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 PTP4A1
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 PTP4A1 from PDB

Differential gene expression and gene-gene network for PTP4A1
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 PTP4A1 and the right PPI network was created from samples without mutations in the LBS of PTP4A1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for PTP4A1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0017661Glomerulonephritis, IGA1Biomarker

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

Pharmacological information for PTP4A1
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 PTP4A1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of PTP4A1
Multiple alignments for Q93096 in multiple species
LBSAA sequence# speciesSpecies
A106AVHCVAGLGRA3Homo sapiens, Mus musculus, Rattus norvegicus
D72DWPFDDGAPPS3Homo sapiens, Mus musculus, Rattus norvegicus
G107VHCVAGLGRAP3Homo sapiens, Mus musculus, Rattus norvegicus
G109CVAGLGRAPVL3Homo sapiens, Mus musculus, Rattus norvegicus
L108HCVAGLGRAPV3Homo sapiens, Mus musculus, Rattus norvegicus
R110VAGLGRAPVLV3Homo sapiens, Mus musculus, Rattus norvegicus
V105IAVHCVAGLGR3Homo sapiens, Mus musculus, Rattus norvegicus

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