mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

Home

Download

 Statistics

Help

About Us

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 KDM6B
Gene summary
Basic gene Info.Gene symbolKDM6B
Gene namelysine (K)-specific demethylase 6B
SynonymsJMJD3
CytomapUCSC genome browser: 17p13.1
Type of geneprotein-coding
RefGenesNM_001080424.1,
DescriptionjmjC domain-containing protein 3jumonji domain containing 3, histone lysine demethylasejumonji domain-containing protein 3lysine demethylase 6Blysine-specific demethylase 6B
Modification date20141207
dbXrefs MIM : 611577
HGNC : HGNC
Ensembl : ENSG00000132510
Vega : OTTHUMG00000178021
ProteinUniProt: O15054
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_KDM6B
BioGPS: 23135
PathwayNCI Pathway Interaction Database: KDM6B
KEGG: KDM6B
REACTOME: KDM6B
Pathway Commons: KDM6B
ContextiHOP: KDM6B
ligand binding site mutation search in PubMed: KDM6B
UCL Cancer Institute: KDM6B
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID


Top
Ligand binding site mutations for KDM6B
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
I1464V1462MUCEC1
N1331D1333EUCEC1
C1578E1577KUCEC1
R1246R1246HUCEC1
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.


Top
Protein structure related information for KDM6B
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
I1464V1462M-1.2701325
R1246R1246H-1.0668153
N1331D1333E-0.89451022
C1578E1577K-0.69453538
(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 KDM6B from PDB

Top
Differential gene expression and gene-gene network for KDM6B
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 KDM6B and the right PPI network was created from samples without mutations in the LBS of KDM6B. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Top

Top
Phenotype information for KDM6B
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0010606Carcinoma, Adenoid Cystic1Biomarker
umls:C3714756Intellectual Disability1Biomarker

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

Top
Pharmacological information for KDM6B
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 KDM6B go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ZNZINC(2+)2xueAC1578
ZNZINC(2+)2xueBC1578
ZNZINC(2+)4askAC1578
ZNZINC(2+)4askBC1578
K0I3-[[2-PYRIDIN-2-YL-6-(1,2,4,5-TETRAHYDRO-3- BENZAZEPIN-3-YL)PYRIMIDIN-4-YL]AMINO]PROPANOIC ACID3-((6-(4,5-DIHYDRO-1H-BENZO[D]AZEPIN-3(2H)- YL)-2-(PYRIDIN-2-YL)PYRIMIDIN-4-YL)AMINO) PROPANOIC ACID4askAR1246 N1331
K0I3-[[2-PYRIDIN-2-YL-6-(1,2,4,5-TETRAHYDRO-3- BENZAZEPIN-3-YL)PYRIMIDIN-4-YL]AMINO]PROPANOIC ACID3-((6-(4,5-DIHYDRO-1H-BENZO[D]AZEPIN-3(2H)- YL)-2-(PYRIDIN-2-YL)PYRIMIDIN-4-YL)AMINO) PROPANOIC ACID4askBR1246 N1331


Top
Conservation information for LBS of KDM6B
Multiple alignments for O15054 in multiple species
LBSAA sequence# speciesSpecies


Copyright © 2016-Present - The University of Texas Health Science Center at Houston
Site Policies | State of Texas