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mutLBSgeneDB |
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| Gene summary for PTPN4 |
 Gene summary |
| Basic gene Info. | Gene symbol | PTPN4 |
| Gene name | protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte) | |
| Synonyms | MEG|PTPMEG|PTPMEG1 | |
| Cytomap | UCSC genome browser: 2q14.2 | |
| Type of gene | protein-coding | |
| RefGenes | NM_002830.3, | |
| Description | PTPase-MEG1megakaryocyte phosphatasemegakaryocyte protein-tyrosine phosphataseprotein tyrosine phosphatase MEG1protein-tyrosine phosphatase MEG1tyrosine-protein phosphatase non-receptor type 4 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 176878 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000088179 | ||
| HPRD : 01471 | ||
| Vega : OTTHUMG00000131436 | ||
| Protein | UniProt: P29074 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PTPN4 | |
| BioGPS: 5775 | ||
| Pathway | NCI Pathway Interaction Database: PTPN4 | |
| KEGG: PTPN4 | ||
| REACTOME: PTPN4 | ||
| Pathway Commons: PTPN4 | ||
| Context | iHOP: PTPN4 | |
| ligand binding site mutation search in PubMed: PTPN4 | ||
| UCL Cancer Institute: PTPN4 | ||
| 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 |
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| Ligand binding site mutations for PTPN4 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | H579 | D580Y | KIRC | 1 | D564 | Q565H | LUAD | 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 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 |
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| 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 | D564 | Q565H | -0.5926603 | H579 | D580Y | -0.58404352 |
| (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 |
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| 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) |
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| Phenotype information for PTPN4 |
| 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 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. |
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| Gene-centered drug-gene interaction network |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Approved | DB00630 | Alendronic acid | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of PTPN4 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | III | Peptide ligand (SER,TRP,GLU,SER,HIS,LYS,SER,GLY,GLY,GLU,THR,ARG,LEU) | 3nfk | A | H579 | III | Peptide ligand (GLY,GLU,THR,ARG,LEU) | 3nfk | B | H579 | III | Peptide ligand (ILE,GLU,SER,ASP,VAL) | 3nfl | A | H579 | III | Peptide ligand (ILE,GLU,SER,ASP,VAL) | 3nfl | B | H579 | III | Peptide ligand (ILE,GLU,SER,ASP,VAL) | 3nfl | C | H579 | III | Peptide ligand (ILE,GLU,SER,ASP,VAL) | 3nfl | D | H579 |
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| Conservation information for LBS of PTPN4 |
| Multiple alignments for P29074 in multiple species |
| LBS | AA sequence | # species | Species | D564 | RLNEGDQVVLI | 2 | Homo sapiens, Mus musculus | D564 | RLNEGDQVLFI | 2 | Caenorhabditis elegans, Caenorhabditis elegans | F528 | DENGRFGFNVK | 2 | Homo sapiens, Mus musculus | F528 | DRHGRFGFNVK | 2 | Caenorhabditis elegans, Caenorhabditis elegans | F530 | NGRFGFNVKGG | 2 | Homo sapiens, Mus musculus | F530 | HGRFGFNVKGG | 2 | Caenorhabditis elegans, Caenorhabditis elegans | G529 | ENGRFGFNVKG | 2 | Homo sapiens, Mus musculus | G529 | RHGRFGFNVKG | 2 | Caenorhabditis elegans, Caenorhabditis elegans | H579 | IAEHTHDQVVL | 2 | Homo sapiens, Mus musculus | H579 | VSTMSHDHVVQ | 2 | Caenorhabditis elegans, Caenorhabditis elegans | I586 | QVVLFIK-ASC | 2 | Homo sapiens, Mus musculus | I586 | HVVQFIRSARS | 2 | Caenorhabditis elegans, Caenorhabditis elegans | K533 | FGFNVKGGYDQ | 2 | Homo sapiens, Mus musculus | K533 | FGFNVKGGADQ | 2 | Caenorhabditis elegans, Caenorhabditis elegans | K587 | VVLFIK-ASCE | 2 | Homo sapiens, Mus musculus | K587 | VVQFIRSARSG | 2 | Caenorhabditis elegans, Caenorhabditis elegans | L584 | HDQVVLFIK-A | 2 | Homo sapiens, Mus musculus | L584 | HDHVVQFIRSA | 2 | Caenorhabditis elegans, Caenorhabditis elegans | N531 | GRFGFNVKGGY | 2 | Homo sapiens, Mus musculus | N531 | GRFGFNVKGGA | 2 | Caenorhabditis elegans, Caenorhabditis elegans | Q538 | KGGYDQKMPVI | 2 | Homo sapiens, Mus musculus | Q538 | KGGADQNYPVI | 2 | Caenorhabditis elegans, Caenorhabditis elegans | R527 | PDENGRFGFNV | 2 | Homo sapiens, Mus musculus | R527 | PDRHGRFGFNV | 2 | Caenorhabditis elegans, Caenorhabditis elegans | S545 | MPVIVSRVAPG | 2 | Homo sapiens, Mus musculus | S545 | YPVIVSRVAPG | 2 | Caenorhabditis elegans, Caenorhabditis elegans | V532 | RFGFNVKGGYD | 2 | Homo sapiens, Mus musculus | V532 | RFGFNVKGGAD | 2 | Caenorhabditis elegans, Caenorhabditis elegans | V583 | THDQVVLFIK- | 2 | Homo sapiens, Mus musculus | V583 | SHDHVVQFIRS | 2 | Caenorhabditis elegans, Caenorhabditis elegans |
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