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 PTPN13
Gene summary
Basic gene Info.Gene symbolPTPN13
Gene nameprotein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)
SynonymsFAP-1|PNP1|PTP-BAS|PTP-BL|PTP1E|PTPL1|PTPLE|hPTP1E
CytomapUCSC genome browser: 4q21.3
Type of geneprotein-coding
RefGenesNM_006264.2,
NM_080683.2,NM_080684.2,NM_080685.2,
Descriptionfas-associated protein-tyrosine phosphatase 1hPTPE1protein-tyrosine phosphatase 1Eprotein-tyrosine phosphatase PTPL1tyrosine-protein phosphatase non-receptor type 13
Modification date20141207
dbXrefs MIM : 600267
HGNC : HGNC
Ensembl : ENSG00000163629
HPRD : 02602
Vega : OTTHUMG00000160968
ProteinUniProt: Q12923
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PTPN13
BioGPS: 5783
PathwayNCI Pathway Interaction Database: PTPN13
KEGG: PTPN13
REACTOME: PTPN13
Pathway Commons: PTPN13
ContextiHOP: PTPN13
ligand binding site mutation search in PubMed: PTPN13
UCL Cancer Institute: PTPN13
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:0006470protein dephosphorylation17657516
GO:0014066regulation of phosphatidylinositol 3-kinase signaling23604317


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Ligand binding site mutations for PTPN13

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
Q2310Q2310EBRCA1
C2408T2406MUCEC1
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 PTPN13
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
C2408T2406M-1.1262271
Q2310Q2310E-0.13933515
(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 PTPN13 from PDB

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Differential gene expression and gene-gene network for PTPN13
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 PTPN13 and the right PPI network was created from samples without mutations in the LBS of PTPN13. 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 PTPN13
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0031117Peripheral Nervous System Diseases2Biomarker

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

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Pharmacological information for PTPN13
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 PTPN13 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
PO4PHOSPHATE ION1wchAC2408
PO4PHOSPHATE ION1wchAQ2310


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Conservation information for LBS of PTPN13
Multiple alignments for Q12923 in multiple species
LBSAA sequence# speciesSpecies


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