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 USP4
Gene summary
Basic gene Info.Gene symbolUSP4
Gene nameubiquitin specific peptidase 4 (proto-oncogene)
CytomapUCSC genome browser: 3p21.3
Type of geneprotein-coding
Descriptiondeubiquitinating 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 date20141207
dbXrefs MIM : 603486
Ensembl : ENSG00000114316
HPRD : 04598
Vega : OTTHUMG00000156825
ProteinUniProt: Q13107
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_USP4
BioGPS: 7375
PathwayNCI Pathway Interaction Database: USP4
Pathway Commons: USP4
ContextiHOP: USP4
ligand binding site mutation search in PubMed: USP4
UCL Cancer Institute: USP4
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0016579protein deubiquitination16316627
GO:0031647regulation of protein stability16472766
GO:0034394protein localization to cell surface16339847

Ligand binding site mutations for USP4

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
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.

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.
LBSAAchange of nsSNVRelative stability change
(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

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)
* Left PPI network was created from samples with mutations in the LBS of USP4 and the right PPI network was created from samples without mutations in the LBS of USP4. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for USP4
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

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 statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of USP4 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of USP4
Multiple alignments for Q13107 in multiple species
LBSAA sequence# speciesSpecies
C461KSTLVCPECAK4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
C461KSTLVCPICNK1Arabidopsis thaliana
C464LVCPECAKVSV4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
C464LVCPICNKVSV1Arabidopsis thaliana
C799HDPWYCPNCKK2Homo sapiens, Bos taurus
C799HDPWYCPTCKK2Mus musculus, Rattus norvegicus
C799DEMWFCPQCNE1Arabidopsis thaliana
C802WYCPNCKKHQQ2Homo sapiens, Bos taurus
C802WYCPTCKKHQQ2Mus musculus, Rattus norvegicus
C802WFCPQCNERRQ1Arabidopsis thaliana

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