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mutLBSgeneDB |
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| Gene summary for USP13 |
 Gene summary |
| Basic gene Info. | Gene symbol | USP13 |
| Gene name | ubiquitin specific peptidase 13 (isopeptidase T-3) | |
| Synonyms | ISOT3|IsoT-3 | |
| Cytomap | UCSC genome browser: 3q26.2-q26.3 | |
| Type of gene | protein-coding | |
| RefGenes | NM_003940.2, | |
| Description | deubiquitinating enzyme 13isopeptidase T-3ubiquitin carboxyl-terminal hydrolase 13ubiquitin specific protease 13 (isopeptidase T-3)ubiquitin thioesterase 13ubiquitin thiolesterase 13ubiquitin-specific-processing protease 13 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 603591 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000058056 | ||
| HPRD : 04666 | ||
| Vega : OTTHUMG00000157783 | ||
| Protein | UniProt: Q92995 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_USP13 | |
| BioGPS: 8975 | ||
| Pathway | NCI Pathway Interaction Database: USP13 | |
| KEGG: USP13 | ||
| REACTOME: USP13 | ||
| Pathway Commons: USP13 | ||
| Context | iHOP: USP13 | |
| ligand binding site mutation search in PubMed: USP13 | ||
| UCL Cancer Institute: USP13 | ||
| 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:0010506 | regulation of autophagy | 21962518 | GO:0050821 | protein stabilization | 21659512 | GO:0070536 | protein K63-linked deubiquitination | 22216260 |
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| Ligand binding site mutations for USP13 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | C214 | D215N | COAD | 1 | H244 | G243V | LUAD | 1 | C211 | K210M | STAD | 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 USP13 |
| 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 | H244 | G243V | 0.1695392 | C214 | D215N | -0.42797135 | C211 | K210M | -0.037547509 |
| (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 USP13 from PDB |
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| Differential gene expression and gene-gene network for USP13 |
| 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 USP13 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0311375 | Arsenic Poisoning | 1 | Biomarker |
| umls:C0037274 | Skin Diseases | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for USP13 |
| 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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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of USP13 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS |
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| Conservation information for LBS of USP13 |
| Multiple alignments for Q92995 in multiple species |
| LBS | AA sequence | # species | Species | C211 | PSGWKCARCDL | 3 | Homo sapiens, Mus musculus, Bos taurus | C211 | PSGWKCAKCEM | 1 | Danio rerio | C214 | WKCARCDLREN | 3 | Homo sapiens, Mus musculus, Bos taurus | C214 | WKCAKCEMREN | 1 | Danio rerio | C231 | DGSVLCGKWFF | 4 | Homo sapiens, Danio rerio, Mus musculus, Bos taurus | H244 | SGGNGHALEHY | 4 | Homo sapiens, Danio rerio, Mus musculus, Bos taurus |
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