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 PTPN4
Gene summary
Basic gene Info.Gene symbolPTPN4
Gene nameprotein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)
CytomapUCSC genome browser: 2q14.2
Type of geneprotein-coding
DescriptionPTPase-MEG1megakaryocyte phosphatasemegakaryocyte protein-tyrosine phosphataseprotein tyrosine phosphatase MEG1protein-tyrosine phosphatase MEG1tyrosine-protein phosphatase non-receptor type 4
Modification date20141207
dbXrefs MIM : 176878
Ensembl : ENSG00000088179
HPRD : 01471
Vega : OTTHUMG00000131436
ProteinUniProt: P29074
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PTPN4
BioGPS: 5775
PathwayNCI Pathway Interaction Database: PTPN4
Pathway Commons: PTPN4
ContextiHOP: PTPN4
ligand binding site mutation search in PubMed: PTPN4
UCL Cancer Institute: PTPN4
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 PTPN4

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 PTPN4
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 PTPN4 from PDB

Differential gene expression and gene-gene network for PTPN4
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 PTPN4 and the right PPI network was created from samples without mutations in the LBS of PTPN4. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for PTPN4
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for PTPN4
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
ApprovedDB00630Alendronic acidSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of PTPN4 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
IIIPeptide ligand (GLY,GLU,THR,ARG,LEU)3nfkBH579
IIIPeptide ligand (ILE,GLU,SER,ASP,VAL)3nflAH579
IIIPeptide ligand (ILE,GLU,SER,ASP,VAL)3nflBH579
IIIPeptide ligand (ILE,GLU,SER,ASP,VAL)3nflCH579
IIIPeptide ligand (ILE,GLU,SER,ASP,VAL)3nflDH579

Conservation information for LBS of PTPN4
Multiple alignments for P29074 in multiple species
LBSAA sequence# speciesSpecies
D564RLNEGDQVVLI2Homo sapiens, Mus musculus
D564RLNEGDQVLFI2Caenorhabditis elegans, Caenorhabditis elegans
F528DENGRFGFNVK2Homo sapiens, Mus musculus
F528DRHGRFGFNVK2Caenorhabditis elegans, Caenorhabditis elegans
F530NGRFGFNVKGG2Homo sapiens, Mus musculus
F530HGRFGFNVKGG2Caenorhabditis elegans, Caenorhabditis elegans
G529ENGRFGFNVKG2Homo sapiens, Mus musculus
G529RHGRFGFNVKG2Caenorhabditis elegans, Caenorhabditis elegans
H579IAEHTHDQVVL2Homo sapiens, Mus musculus
H579VSTMSHDHVVQ2Caenorhabditis elegans, Caenorhabditis elegans
I586QVVLFIK-ASC2Homo sapiens, Mus musculus
I586HVVQFIRSARS2Caenorhabditis elegans, Caenorhabditis elegans
K533FGFNVKGGYDQ2Homo sapiens, Mus musculus
K533FGFNVKGGADQ2Caenorhabditis elegans, Caenorhabditis elegans
K587VVLFIK-ASCE2Homo sapiens, Mus musculus
K587VVQFIRSARSG2Caenorhabditis elegans, Caenorhabditis elegans
L584HDQVVLFIK-A2Homo sapiens, Mus musculus
L584HDHVVQFIRSA2Caenorhabditis elegans, Caenorhabditis elegans
N531GRFGFNVKGGY2Homo sapiens, Mus musculus
N531GRFGFNVKGGA2Caenorhabditis elegans, Caenorhabditis elegans
Q538KGGYDQKMPVI2Homo sapiens, Mus musculus
Q538KGGADQNYPVI2Caenorhabditis elegans, Caenorhabditis elegans
R527PDENGRFGFNV2Homo sapiens, Mus musculus
R527PDRHGRFGFNV2Caenorhabditis elegans, Caenorhabditis elegans
S545MPVIVSRVAPG2Homo sapiens, Mus musculus
S545YPVIVSRVAPG2Caenorhabditis elegans, Caenorhabditis elegans
V532RFGFNVKGGYD2Homo sapiens, Mus musculus
V532RFGFNVKGGAD2Caenorhabditis elegans, Caenorhabditis elegans
V583THDQVVLFIK-2Homo sapiens, Mus musculus
V583SHDHVVQFIRS2Caenorhabditis elegans, Caenorhabditis elegans

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