mutLBSgeneDB |
Gene summary for USP4 |
Gene summary |
Basic gene Info. | Gene symbol | USP4 |
Gene name | ubiquitin specific peptidase 4 (proto-oncogene) | |
Synonyms | UNP|Unph | |
Cytomap | UCSC genome browser: 3p21.3 | |
Type of gene | protein-coding | |
RefGenes | NM_001251877.1, NM_003363.3,NM_199443.2, | |
Description | deubiquitinating enzyme 4ubiquitin carboxyl-terminal esterase 4ubiquitin carboxyl-terminal hydrolase 4ubiquitin specific protease 4 (proto-oncogene)ubiquitin thioesterase 4ubiquitin thiolesterase 4ubiquitin-specific processing protease 4ubiquitous | |
Modification date | 20141207 | |
dbXrefs | MIM : 603486 | |
HGNC : HGNC | ||
Ensembl : ENSG00000114316 | ||
HPRD : 04598 | ||
Vega : OTTHUMG00000156825 | ||
Protein | UniProt: Q13107 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_USP4 | |
BioGPS: 7375 | ||
Pathway | NCI Pathway Interaction Database: USP4 | |
KEGG: USP4 | ||
REACTOME: USP4 | ||
Pathway Commons: USP4 | ||
Context | iHOP: USP4 | |
ligand binding site mutation search in PubMed: USP4 | ||
UCL Cancer Institute: USP4 | ||
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:0016579 | protein deubiquitination | 16316627 | GO:0031647 | regulation of protein stability | 16472766 | GO:0034394 | protein localization to cell surface | 16339847 |
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Ligand binding site mutations for USP4 |
Cancer type specific mutLBS sorted by frequency |
LBS | AAchange of nsSNV | Cancer type | # samples | C799 | C799W | 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 USP4 |
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 | C799 | C799W | -0.949452 |
(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 USP4 from PDB |
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Differential gene expression and gene-gene network for USP4 |
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 USP4 |
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 USP4 |
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 USP4 go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ZN | ZINC(2+) | 2y6e | A | C799 | ZN | ZINC(2+) | 2y6e | B | C799 | ZN | ZINC(2+) | 2y6e | C | C799 | ZN | ZINC(2+) | 2y6e | D | C799 |
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Conservation information for LBS of USP4 |
Multiple alignments for Q13107 in multiple species |
LBS | AA sequence | # species | Species | C461 | KSTLVCPECAK | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus | C461 | KSTLVCPICNK | 1 | Arabidopsis thaliana | C464 | LVCPECAKVSV | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus | C464 | LVCPICNKVSV | 1 | Arabidopsis thaliana | C799 | HDPWYCPNCKK | 2 | Homo sapiens, Bos taurus | C799 | HDPWYCPTCKK | 2 | Mus musculus, Rattus norvegicus | C799 | DEMWFCPQCNE | 1 | Arabidopsis thaliana | C802 | WYCPNCKKHQQ | 2 | Homo sapiens, Bos taurus | C802 | WYCPTCKKHQQ | 2 | Mus musculus, Rattus norvegicus | C802 | WFCPQCNERRQ | 1 | Arabidopsis thaliana |
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