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mutLBSgeneDB |
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| Gene summary for USP5 |
 Gene summary |
| Basic gene Info. | Gene symbol | USP5 |
| Gene name | ubiquitin specific peptidase 5 (isopeptidase T) | |
| Synonyms | ISOT | |
| Cytomap | UCSC genome browser: 12p13 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001098536.1, NM_003481.2, | |
| Description | deubiquitinating enzyme 5isopeptidase Tubiquitin carboxyl-terminal hydrolase 5ubiquitin isopeptidase Tubiquitin specific protease 5 (isopeptidase T)ubiquitin thioesterase 5ubiquitin thiolesterase 5ubiquitin-specific protease-5 (ubiquitin isopeptida | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 601447 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000111667 | ||
| HPRD : 03265 | ||
| Vega : OTTHUMG00000169233 | ||
| Protein | UniProt: P45974 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_USP5 | |
| BioGPS: 8078 | ||
| Pathway | NCI Pathway Interaction Database: USP5 | |
| KEGG: USP5 | ||
| REACTOME: USP5 | ||
| Pathway Commons: USP5 | ||
| Context | iHOP: USP5 | |
| ligand binding site mutation search in PubMed: USP5 | ||
| UCL Cancer Institute: USP5 | ||
| Assigned class in mutLBSgeneDB | A: This gene has a literature evidence and it belongs to targetable_mutLBSgenes. | |
| References showing study about ligand binding site mutation for USP5. | 1. "Reyes-Turcu FE, Shanks JR, Komander D, Wilkinson KD. Recognition of polyubiquitin isoforms by the multiple ubiquitin binding modules of isopeptidase T. J Biol Chem. 2008 Jul 11;283(28):19581-92. doi: 10.1074/jbc.M800947200. Epub 2008 May 15." 18482987 | |
| 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 USP5 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | Q433 | Q433L | LUAD | 1 | C199 | W197C | 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 USP5 |
| 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 | Q433 | Q433L | 0.002136186 | C199 | W197C | -1.2948616 |
| (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 USP5 from PDB |
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| Differential gene expression and gene-gene network for USP5 |
| 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 USP5 |
| 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 USP5 |
| 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 USP5 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ZN | ZINC(2+) | 2g45 | A | C199 | ZN | ZINC(2+) | 2g45 | D | C199 | ZN | ZINC(2+) | 3ihp | A | C199 | ZN | ZINC(2+) | 3ihp | B | C199 | NEH | ETHYLAMINE | 3ihp | A | Q433 | NEH | ETHYLAMINE | 3ihp | B | Q433 |
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| Conservation information for LBS of USP5 |
| Multiple alignments for P45974 in multiple species |
| LBS | AA sequence | # species | Species | C199 | PCGWKCSKCDM | 2 | Homo sapiens, Mus musculus | C199 | PSGWKCSKCDK | 1 | Arabidopsis thaliana | C202 | WKCSKCDMREN | 2 | Homo sapiens, Mus musculus | C202 | WKCSKCDKTEN | 1 | Arabidopsis thaliana | C219 | DGSILCGRRYF | 2 | Homo sapiens, Mus musculus | C219 | DGMILCGRKNW | 1 | Arabidopsis thaliana | C335 | NLGNSCYLNSV | 2 | Homo sapiens, Mus musculus | C335 | NLGNSCYLAAT | 1 | Arabidopsis thaliana | G817 | TSTMCGHYVCH | 2 | Homo sapiens, Mus musculus | G817 | TSVHCGHYVAH | 1 | Arabidopsis thaliana | H232 | SGGNNHAVEHY | 2 | Homo sapiens, Mus musculus | H232 | TGGNNHAVEHY | 1 | Arabidopsis thaliana | N333 | IRNLGNSCYLN | 2 | Homo sapiens, Mus musculus | N333 | LVNLGNSCYLA | 1 | Arabidopsis thaliana | Q433 | FSTNRQQDAQE | 2 | Homo sapiens, Mus musculus | Q433 | FSSMRQQDALD | 1 | Arabidopsis thaliana |
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