mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 LIG3
Gene summary
Basic gene Info.Gene symbolLIG3
Gene nameligase III, DNA, ATP-dependent
SynonymsLIG2
CytomapUCSC genome browser: 17q11.2-q12
Type of geneprotein-coding
RefGenesNM_002311.4,
NM_013975.3,
DescriptionDNA ligase 3ligase II, DNA, ATP-dependentpolydeoxyribonucleotide synthase [ATP] 3
Modification date20141207
dbXrefs MIM : 600940
HGNC : HGNC
Ensembl : ENSG00000005156
HPRD : 02966
Vega : OTTHUMG00000128519
ProteinUniProt: P49916
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LIG3
BioGPS: 3980
PathwayNCI Pathway Interaction Database: LIG3
KEGG: LIG3
REACTOME: LIG3
Pathway Commons: LIG3
ContextiHOP: LIG3
ligand binding site mutation search in PubMed: LIG3
UCL Cancer Institute: LIG3
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:0033151V(D)J recombination9809069


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Ligand binding site mutations for LIG3

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
N322,N320L321FBLCA1
H733H733YLUAD1
F595D596HLUAD1
G732,A730G731ELUSC1
I710I710VOV1
H795T796KOV1
K704G706SSKCM1
G700Y699CSTAD1
K531V533ISTAD1
C108K107TSTAD1
G425A426VSTAD1
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 LIG3
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
K704G706S-1.2127206
N320L321F-1.0712567
N322L321F-1.0712567
G425A426V-1.0551956
K531V533I-0.98394908
F595D596H-0.83837232
C108K107T-0.66139492
I710I710V-0.50590702
G732G731E-0.46153443
A730G731E-0.46153443
G700Y699C-0.27903216
H733H733Y-0.095353546
H795T796K-0.074268357
(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 LIG3 from PDB

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Differential gene expression and gene-gene network for LIG3
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 LIG3 and the right PPI network was created from samples without mutations in the LBS of LIG3. 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 LIG3
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

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Pharmacological information for LIG3
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.

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
ApprovedDB00290BleomycinSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of LIG3 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS


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Conservation information for LBS of LIG3
Multiple alignments for P49916 in multiple species
LBSAA sequence# speciesSpecies


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