mutLBSgeneDB |
Gene summary for PTPN9 |
Gene summary |
Basic gene Info. | Gene symbol | PTPN9 |
Gene name | protein tyrosine phosphatase, non-receptor type 9 | |
Synonyms | MEG2|PTPMEG2 | |
Cytomap | UCSC genome browser: 15q24.2 | |
Type of gene | protein-coding | |
RefGenes | NM_002833.3, | |
Description | PTPase MEG2PTPase-MEG2protein-tyrosine phosphatase MEG2tyrosine-protein phosphatase non-receptor type 9 | |
Modification date | 20141207 | |
dbXrefs | MIM : 600768 | |
HGNC : HGNC | ||
Ensembl : ENSG00000169410 | ||
HPRD : 02864 | ||
Protein | UniProt: P43378 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PTPN9 | |
BioGPS: 5780 | ||
Pathway | NCI Pathway Interaction Database: PTPN9 | |
KEGG: PTPN9 | ||
REACTOME: PTPN9 | ||
Pathway Commons: PTPN9 | ||
Context | iHOP: PTPN9 | |
ligand binding site mutation search in PubMed: PTPN9 | ||
UCL Cancer Institute: PTPN9 | ||
Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO Term | PubMed ID | GO:0035335 | peptidyl-tyrosine dephosphorylation | 19167335 |
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Ligand binding site mutations for PTPN9 |
Cancer type specific mutLBS sorted by frequency |
LBS | AAchange of nsSNV | Cancer type | # samples | R311 | R311H | COAD | 2 | E308 | D309H | BLCA | 1 | Y471 | P469T | BLCA | 1 | R311 | R311C | COAD | 1 | R311 | R312C | UCEC | 1 | R311,P315 | E313K | UCEC | 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 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. |
LBS | AAchange of nsSNV | Relative stability change | R311 | R311H | -1.4747806 | Y471 | P469T | -1.364833 | R311 | R311C | -1.2155339 | P315 | E313K | -1.0775958 | R311 | E313K | -1.0775958 | E308 | D309H | -0.80016495 | R311 | R312C | -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 ID | PDB title | PDB structure | 2PA5 | Crystal 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) |
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Phenotype information for PTPN9 |
Gene level disease information (DisGeNet) |
Disease ID | Disease name | # PubMed | Association type |
Mutation level pathogenic information (ClinVar annotation) |
Allele ID | AA change | Clinical significance | Origin | Phenotype 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 status | DrugBank ID | Name | Type | Drug structure |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of PTPN9 go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | B26 | N-(4-BROMO-3-METHYLBENZOYL)-4-[DIFLUORO(PHOSPHONO) METHYL]-L-PHENYLALANYL-N~5~-(3-IODOBENZOYL)-L- ORNITHYL-3-{[(4-HYDROXY-3-METHOXYPHENYL)ACETYL]AMINO}- D-ALANINAMIDE | 4ge6 | A | E308 R311 P315 | 75A | N-ACETYL-4-[DIFLUORO(PHOSPHONO)METHYL]-L-PHENYLALANYL- N~5~-(3-IODOBENZOYL)-L-ORNITHINAMIDE | 4ge2 | A | P315 | A89 | N-(4-BROMO-3-METHYLBENZOYL)-4-[DIFLUORO(PHOSPHONO) METHYL]-L-PHENYLALANYL-N~5~-(3-IODOBENZOYL)-L- ORNITHINAMIDE | 4ge5 | A | R311 P315 | III | Peptide ligand (ASN,LEU,TYR,TYR,TRP) | 4icz | A | Y471 |
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Conservation information for LBS of PTPN9 |
Multiple alignments for P43378 in multiple species |
LBS | AA sequence | # species | Species | A517 | VVHCSAGIGRT | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | C515 | PIVVHCSAGIG | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | D335 | KNRYGDVPCLD | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | E308 | IYEEYEDIRRE | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | F556 | RTQRAFSIQTP | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | G334 | EKNRYGDVPCL | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | G518 | VHCSAGIGRTG | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | G520 | CSAGIGRTGTF | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | I519 | HCSAGIGRTGT | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | P315 | IRRENPVGTFH | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | P561 | FSIQTPEQYYF | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | Q559 | RAFSIQTPEQY | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | R311 | EYEDIRRENPV | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | R332 | NLEKNRYGDVP | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | R410 | EEGGRRKCGQY | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | R521 | SAGIGRTGTFC | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | S516 | IVVHCSAGIGR | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | V336 | NRYGDVPCLDQ | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | Y304 | QKQGIYEEYED | 2 | Homo sapiens, Rattus norvegicus | Y304 | QKRGIYEEYED | 1 | Mus musculus | Y333 | LEKNRYGDVPC | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | Y471 | LSWPDYGVPSS | 3 | Homo sapiens, Rattus norvegicus, Mus musculus |
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