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 PTPN9
Gene summary
Basic gene Info.Gene symbolPTPN9
Gene nameprotein tyrosine phosphatase, non-receptor type 9
SynonymsMEG2|PTPMEG2
CytomapUCSC genome browser: 15q24.2
Type of geneprotein-coding
RefGenesNM_002833.3,
DescriptionPTPase MEG2PTPase-MEG2protein-tyrosine phosphatase MEG2tyrosine-protein phosphatase non-receptor type 9
Modification date20141207
dbXrefs MIM : 600768
HGNC : HGNC
Ensembl : ENSG00000169410
HPRD : 02864
ProteinUniProt: P43378
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PTPN9
BioGPS: 5780
PathwayNCI Pathway Interaction Database: PTPN9
KEGG: PTPN9
REACTOME: PTPN9
Pathway Commons: PTPN9
ContextiHOP: PTPN9
ligand binding site mutation search in PubMed: PTPN9
UCL Cancer Institute: PTPN9
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0035335peptidyl-tyrosine dephosphorylation19167335


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Ligand binding site mutations for PTPN9

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
R311R311HCOAD2
E308D309HBLCA1
Y471P469TBLCA1
R311R311CCOAD1
R311R312CUCEC1
R311,P315E313KUCEC1
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 PTPN9
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
R311R311H-1.4747806
Y471P469T-1.364833
R311R311C-1.2155339
P315E313K-1.0775958
R311E313K-1.0775958
E308D309H-0.80016495
R311R312C-0.75432703
(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 PTPN9 from PDB
PDB IDPDB titlePDB structure
2PA5Crystal structure of human protein tyrosine phosphatase PTPN9

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Differential gene expression and gene-gene network for PTPN9
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 PTPN9 and the right PPI network was created from samples without mutations in the LBS of PTPN9. 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 PTPN9
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

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Pharmacological information for PTPN9
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 PTPN9 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
B26N-(4-BROMO-3-METHYLBENZOYL)-4-[DIFLUORO(PHOSPHONO) METHYL]-L-PHENYLALANYL-N~5~-(3-IODOBENZOYL)-L- ORNITHYL-3-{[(4-HYDROXY-3-METHOXYPHENYL)ACETYL]AMINO}- D-ALANINAMIDE4ge6AE308 R311 P315
75AN-ACETYL-4-[DIFLUORO(PHOSPHONO)METHYL]-L-PHENYLALANYL- N~5~-(3-IODOBENZOYL)-L-ORNITHINAMIDE4ge2AP315
A89N-(4-BROMO-3-METHYLBENZOYL)-4-[DIFLUORO(PHOSPHONO) METHYL]-L-PHENYLALANYL-N~5~-(3-IODOBENZOYL)-L- ORNITHINAMIDE4ge5AR311 P315
IIIPeptide ligand (ASN,LEU,TYR,TYR,TRP)4iczAY471


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Conservation information for LBS of PTPN9
Multiple alignments for P43378 in multiple species
LBSAA sequence# speciesSpecies
A517VVHCSAGIGRT3Homo sapiens, Rattus norvegicus, Mus musculus
C515PIVVHCSAGIG3Homo sapiens, Rattus norvegicus, Mus musculus
D335KNRYGDVPCLD3Homo sapiens, Rattus norvegicus, Mus musculus
E308IYEEYEDIRRE3Homo sapiens, Rattus norvegicus, Mus musculus
F556RTQRAFSIQTP3Homo sapiens, Rattus norvegicus, Mus musculus
G334EKNRYGDVPCL3Homo sapiens, Rattus norvegicus, Mus musculus
G518VHCSAGIGRTG3Homo sapiens, Rattus norvegicus, Mus musculus
G520CSAGIGRTGTF3Homo sapiens, Rattus norvegicus, Mus musculus
I519HCSAGIGRTGT3Homo sapiens, Rattus norvegicus, Mus musculus
P315IRRENPVGTFH3Homo sapiens, Rattus norvegicus, Mus musculus
P561FSIQTPEQYYF3Homo sapiens, Rattus norvegicus, Mus musculus
Q559RAFSIQTPEQY3Homo sapiens, Rattus norvegicus, Mus musculus
R311EYEDIRRENPV3Homo sapiens, Rattus norvegicus, Mus musculus
R332NLEKNRYGDVP3Homo sapiens, Rattus norvegicus, Mus musculus
R410EEGGRRKCGQY3Homo sapiens, Rattus norvegicus, Mus musculus
R521SAGIGRTGTFC3Homo sapiens, Rattus norvegicus, Mus musculus
S516IVVHCSAGIGR3Homo sapiens, Rattus norvegicus, Mus musculus
V336NRYGDVPCLDQ3Homo sapiens, Rattus norvegicus, Mus musculus
Y304QKQGIYEEYED2Homo sapiens, Rattus norvegicus
Y304QKRGIYEEYED1Mus musculus
Y333LEKNRYGDVPC3Homo sapiens, Rattus norvegicus, Mus musculus
Y471LSWPDYGVPSS3Homo sapiens, Rattus norvegicus, Mus musculus


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