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 CBX3
Gene summary
Basic gene Info.Gene symbolCBX3
Gene namechromobox homolog 3
SynonymsHECH|HP1-GAMMA|HP1Hs-gamma
CytomapUCSC genome browser: 7p15.2
Type of geneprotein-coding
RefGenesNM_007276.4,
NM_016587.3,
DescriptionHP1 gamma homologchromobox homolog 3 (HP1 gamma homolog, Drosophila)chromobox protein homolog 3heterochromatin protein 1 homolog gammaheterochromatin protein HP1 gammaheterochromatin-like protein 1modifier 2 protein
Modification date20141207
dbXrefs MIM : 604477
HGNC : HGNC
Ensembl : ENSG00000122565
HPRD : 05130
Vega : OTTHUMG00000022911
ProteinUniProt: Q13185
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CBX3
BioGPS: 11335
PathwayNCI Pathway Interaction Database: CBX3
KEGG: CBX3
REACTOME: CBX3
Pathway Commons: CBX3
ContextiHOP: CBX3
ligand binding site mutation search in PubMed: CBX3
UCL Cancer Institute: CBX3
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:0045892negative regulation of transcription, DNA-templated9636147


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Ligand binding site mutations for CBX3
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
C69C69RCOAD1
W51W51CCOAD1
L72I73NUCEC1
V32V32MUCEC1
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 CBX3
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
W51W51C-1.3706523
C69C69R-1.0330694
L72I73N-0.98964119
V32V32M-0.57793771
(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 CBX3 from PDB

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Differential gene expression and gene-gene network for CBX3
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 CBX3 and the right PPI network was created from samples without mutations in the LBS of CBX3. 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 CBX3
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 CBX3
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 CBX3 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
IIIPeptide ligand (VAL,HIS,ARG,ALA,ARG,LYS,THR,MET,SER,LYS)3dm1CV32 W51
IIIPeptide ligand (LYS,VAL,HIS,ARG,ALA,ARG,LYS)3dm1GV32 W51
IIIPeptide ligand (LYS,VAL,HIS,ARG,ALA,ARG,LYS,THR)3dm1AV32 W51 C69
IIIPeptide ligand (LYS,VAL,HIS,ARG,ALA,ARG,LYS,THR,MET)3dm1EV32 W51 C69
IIIPeptide ligand (TYR,PRO,VAL,LYS,LYS,LYS,ALA,ARG,LYS,SER,ALA,GLY)3tzdAV32 W51 L72


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Conservation information for LBS of CBX3
Multiple alignments for Q13185 in multiple species
LBSAA sequence# speciesSpecies


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