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 RNF4
Gene summary
Basic gene Info.Gene symbolRNF4
Gene namering finger protein 4
CytomapUCSC genome browser: 4p16.3
Type of geneprotein-coding
DescriptionE3 ubiquitin ligase RNF4E3 ubiquitin-protein ligase RNF4small nuclear RING finger protein
Modification date20141207
dbXrefs MIM : 602850
Ensembl : ENSG00000063978
HPRD : 04167
Vega : OTTHUMG00000160516
ProteinUniProt: P78317
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RNF4
BioGPS: 6047
PathwayNCI Pathway Interaction Database: RNF4
Pathway Commons: RNF4
ContextiHOP: RNF4
ligand binding site mutation search in PubMed: RNF4
UCL Cancer Institute: RNF4
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0045944positive regulation of transcription from RNA polymerase II promoter12885770
GO:0046685response to arsenic-containing substance20943951

Ligand binding site mutations for RNF4
Lollipop-style diagram of mutations at LBS in amino-acid sequence.
We represented ligand binding site mutations only. (You can see big image via clicking.)
: non-synonymous mutation on LBS, Circle size denotes number of samples.

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 RNF4
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 RNF4 from PDB

Differential gene expression and gene-gene network for RNF4
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 RNF4 and the right PPI network was created from samples without mutations in the LBS of RNF4. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for RNF4
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for RNF4
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 RNF4 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of RNF4
Multiple alignments for P78317 in multiple species
LBSAA sequence# speciesSpecies
C132SGTVSCPICMD3Homo sapiens, Mus musculus, Rattus norvegicus
C135VSCPICMDGYS3Homo sapiens, Mus musculus, Rattus norvegicus
C154IVSTECGHVFC3Homo sapiens, Mus musculus, Rattus norvegicus
C159CGHVFCSQCLR3Homo sapiens, Mus musculus, Rattus norvegicus
C162VFCSQCLRDSL3Homo sapiens, Mus musculus, Rattus norvegicus
C173KNANTCPTCRK3Homo sapiens, Mus musculus, Rattus norvegicus
C176NTCPTCRKKIN3Homo sapiens, Mus musculus, Rattus norvegicus
H156STECGHVFCSQ3Homo sapiens, Mus musculus, Rattus norvegicus

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