mutLBSgeneDB

mutLBSgeneDB
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 DDX58
Gene summary
Basic gene Info.Gene symbolDDX58
Gene nameDEAD (Asp-Glu-Ala-Asp) box polypeptide 58
SynonymsRIG-I|RIGI|RLR-1
CytomapUCSC genome browser: 9p12
Type of geneprotein-coding
RefGenesNM_014314.3,
DescriptionDEAD box protein 58DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptideRNA helicase RIG-Iprobable ATP-dependent RNA helicase DDX58retinoic acid-inducible gene 1 proteinretinoic acid-inducible gene I protein
Modification date20141222
dbXrefs MIM : 609631
HGNC : HGNC
Ensembl : ENSG00000107201
HPRD : 13131
Vega : OTTHUMG00000019746
ProteinUniProt: O95786
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DDX58
BioGPS: 23586
PathwayNCI Pathway Interaction Database: DDX58
KEGG: DDX58
REACTOME: DDX58
Pathway Commons: DDX58
ContextiHOP: DDX58
ligand binding site mutation search in PubMed: DDX58
UCL Cancer Institute: DDX58
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0009597detection of virus17079289
GO:0030334regulation of cell migration19122199
GO:0032727positive regulation of interferon-alpha production19576794
GO:0032728positive regulation of interferon-beta production17079289
GO:0042993positive regulation of transcription factor import into nucleus17079289
GO:0045944positive regulation of transcription from RNA polymerase II promoter17079289


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Ligand binding site mutations for DDX58
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
C864R866QCOAD2
K861I862MCOAD1
N353N354KLUSC1
R244R244IUCEC1
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 DDX58
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
C864R866Q-1.0517541
N353N354K-0.82572253
K861I862M-0.62855415
R244R244I-0.40610354
(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 DDX58 from PDB
PDB IDPDB titlePDB structure
2YKGSTRUCTURAL INSIGHTS INTO RNA RECOGNITION BY RIG-I

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Differential gene expression and gene-gene network for DDX58
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 DDX58 and the right PPI network was created from samples without mutations in the LBS of DDX58. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


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Phenotype information for DDX58
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0021400Influenza, Human13AlteredExpression, Biomarker
umls:C0019196Hepatitis C11Biomarker, GeneticVariation
umls:C0242656Disease Progression1Biomarker
umls:C0033860Psoriasis1Biomarker

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

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Pharmacological information for DDX58
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 DDX58 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ZNZINC(2+)2qfbAC864
ZNZINC(2+)2qfbBC864
ZNZINC(2+)2qfbCC864
ZNZINC(2+)2qfbDC864
ZNZINC(2+)2qfbEC864
ZNZINC(2+)2qfbFC864
ZNZINC(2+)2qfbGC864
ZNZINC(2+)2qfbHC864
ZNZINC(2+)2qfbIC864
ZNZINC(2+)2qfbJC864
ZNZINC(2+)2ykgAC864
ZNZINC(2+)3lrnAC864
ZNZINC(2+)3lrnBC864
ZNZINC(2+)3lrrAC864
ZNZINC(2+)3lrrBC864
ZNZINC(2+)3ncuAC864
ZNZINC(2+)3ncuBC864
ZNZINC(2+)3og8AC864
ZNZINC(2+)3og8BC864
ZNZINC(2+)3tmiAC864
ZNZINC(2+)4ay2AC864
ZNZINC(2+)4bpbAC864
ZNZINC(2+)3zd6AC864
ZNZINC(2+)3zd7AC864
ZNZINC(2+)5e3hAC864
ZNZINC(2+)5f98AC864
ZNZINC(2+)5f98CC864
ZNZINC(2+)5f98EC864
ZNZINC(2+)5f98GC864
ZNZINC(2+)5f98IC864
ZNZINC(2+)5f98KC864
ZNZINC(2+)5f9fAC864
ZNZINC(2+)5f9fCC864
ZNZINC(2+)5f9fEC864
ZNZINC(2+)5f9fGC864
ZNZINC(2+)5f9fIC864
ZNZINC(2+)5f9fKC864
ZNZINC(2+)5f9hAC864
ZNZINC(2+)5f9hCC864
ZNZINC(2+)5f9hEC864
ZNZINC(2+)5f9hGC864
ZNZINC(2+)5f9hIC864
ZNZINC(2+)5f9hKC864
NUCNucleic Acids3lrnAK861
NUCNucleic Acids3lrnBK861
NUCNucleic Acids3lrrAK861
NUCNucleic Acids3lrrBK861
NUCNucleic Acids3ncuAK861
NUCNucleic Acids3ncuBK861
M7G7-METHYL-7,8-DIHYDROGUANOSINE-5'-DIPHOSPHATE5f98AK861
M7G7-METHYL-7,8-DIHYDROGUANOSINE-5'-DIPHOSPHATE5f98CK861
M7G7-METHYL-7,8-DIHYDROGUANOSINE-5'-DIPHOSPHATE5f98EK861
NUCNucleic Acids5f98GK861
M7G7-METHYL-7,8-DIHYDROGUANOSINE-5'-DIPHOSPHATE5f98GK861
NUCNucleic Acids5f98IK861
M7G7-METHYL-7,8-DIHYDROGUANOSINE-5'-DIPHOSPHATE5f98IK861
M7G7-METHYL-7,8-DIHYDROGUANOSINE-5'-DIPHOSPHATE5f98KK861
GTPGTP5f9hAK861
GTPGTP5f9hCK861
GTPGTP5f9hEK861
GTPGTP5f9hGK861
GTPGTP5f9hIK861
GTPGTP5f9hKK861
NUCNucleic Acids2ykgAN353
NUCNucleic Acids3tmiAN353
NUCNucleic Acids4bpbAN353
NUCNucleic Acids3zd7AN353
NUCNucleic Acids5e3hAN353
NUCNucleic Acids5f98EN353
NUCNucleic Acids5f9fAN353
NUCNucleic Acids5f9fCN353
NUCNucleic Acids5f9fGN353
BU3(R,R)-BUTANE-2,3-DIOL5f9fGN353
NUCNucleic Acids5f9fIN353
NUCNucleic Acids5f9fKN353
NUCNucleic Acids5f9hAN353
NUCNucleic Acids5f9hEN353
NUCNucleic Acids5f9hGN353
NUCNucleic Acids5f9hIN353
NUCNucleic Acids5f9hKN353
NUCNucleic Acids4ay2AN353 K861
NUCNucleic Acids5f98AN353 K861
NUCNucleic Acids5f98CN353 K861
ADPADP3tmiAR244
ADPADP4ay2AR244
ADPADP3zd7AR244
ADPADP5e3hAR244


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Conservation information for LBS of DDX58
Multiple alignments for O95786 in multiple species
LBSAA sequence# speciesSpecies


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