mutLBSgeneDB |
Gene summary for RNF4 |
Gene summary |
Basic gene Info. | Gene symbol | RNF4 |
Gene name | ring finger protein 4 | |
Synonyms | SLX5|SNURF | |
Cytomap | UCSC genome browser: 4p16.3 | |
Type of gene | protein-coding | |
RefGenes | NM_001185009.2, NM_001185010.2,NM_002938.4, | |
Description | E3 ubiquitin ligase RNF4E3 ubiquitin-protein ligase RNF4small nuclear RING finger protein | |
Modification date | 20141207 | |
dbXrefs | MIM : 602850 | |
HGNC : HGNC | ||
Ensembl : ENSG00000063978 | ||
HPRD : 04167 | ||
Vega : OTTHUMG00000160516 | ||
Protein | UniProt: P78317 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RNF4 | |
BioGPS: 6047 | ||
Pathway | NCI Pathway Interaction Database: RNF4 | |
KEGG: RNF4 | ||
REACTOME: RNF4 | ||
Pathway Commons: RNF4 | ||
Context | iHOP: RNF4 | |
ligand binding site mutation search in PubMed: RNF4 | ||
UCL Cancer Institute: RNF4 | ||
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:0045944 | positive regulation of transcription from RNA polymerase II promoter | 12885770 | GO:0046685 | response to arsenic-containing substance | 20943951 |
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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 |
LBS | AAchange of nsSNV | Cancer type | # samples | C162 | R164C | UCEC | 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 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. |
LBS | AAchange of nsSNV | Relative stability change | C162 | R164C | -0.83573551 |
(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 |
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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) |
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Phenotype information for RNF4 |
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 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 status | DrugBank ID | Name | Type | Drug structure |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of RNF4 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 RNF4 |
Multiple alignments for P78317 in multiple species |
LBS | AA sequence | # species | Species | C132 | SGTVSCPICMD | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C135 | VSCPICMDGYS | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C154 | IVSTECGHVFC | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C159 | CGHVFCSQCLR | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C162 | VFCSQCLRDSL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C173 | KNANTCPTCRK | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C176 | NTCPTCRKKIN | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | H156 | STECGHVFCSQ | 3 | Homo sapiens, Mus musculus, Rattus norvegicus |
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