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 KDM2A
Gene summary
Basic gene Info.Gene symbolKDM2A
Gene namelysine (K)-specific demethylase 2A
CytomapUCSC genome browser: 11q13.2
Type of geneprotein-coding
DescriptionCXXC-type zinc finger protein 8F-box and leucine-rich repeat protein 11F-box/LRR-repeat protein 11[Histone-H3]-lysine-36 demethylase 1AjmjC domain-containing histone demethylation protein 1Ajumonji C domain-containing histone demethylase 1Alysine-sp
Modification date20141207
dbXrefs MIM : 605657
Ensembl : ENSG00000173120
HPRD : 05741
Vega : OTTHUMG00000167103
ProteinUniProt: Q9Y2K7
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_KDM2A
BioGPS: 22992
PathwayNCI Pathway Interaction Database: KDM2A
Pathway Commons: KDM2A
ContextiHOP: KDM2A
ligand binding site mutation search in PubMed: KDM2A
UCL Cancer Institute: KDM2A
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

Ligand binding site mutations for KDM2A
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
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.

Protein structure related information for KDM2A
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
(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 KDM2A from PDB

Differential gene expression and gene-gene network for KDM2A
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 KDM2A and the right PPI network was created from samples without mutations in the LBS of KDM2A. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for KDM2A
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for KDM2A
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 KDM2A go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of KDM2A
Multiple alignments for Q9Y2K7 in multiple species
LBSAA sequence# speciesSpecies
C582CVQGECGVCHY2Homo sapiens, Mus musculus
C582CQRSDCGTCPF1Drosophila melanogaster
C582CVQRECGTCHY1Xenopus tropicalis
C585GECGVCHYCRD2Homo sapiens, Mus musculus
C585SDCGTCPFCMD1Drosophila melanogaster
C585RECGTCHYCKD1Xenopus tropicalis
C588GVCHYCRDMKK2Homo sapiens, Mus musculus
C588GTCPFCMDMVK1Drosophila melanogaster
C588GTCHYCKDMKK1Xenopus tropicalis
C604RMKQSCVLRQC3Homo sapiens, Xenopus tropicalis, Mus musculus
C604RAKQTCMMRQC1Drosophila melanogaster
C620PHSVTCSLC--2Homo sapiens, Mus musculus
C620PVTAQCVYCHL1Drosophila melanogaster
C620PHSVTCALC--1Xenopus tropicalis
C623VTCSLC-----2Homo sapiens, Mus musculus
C623AQCVYCHLDGW1Drosophila melanogaster
C623VTCALC-----1Xenopus tropicalis
C653IVHPGCL--QM2Homo sapiens, Mus musculus
C653IAHPDCALSQL1Drosophila melanogaster
C653IVHPGCL--EM1Xenopus tropicalis
D214TDFHVDFGGTS3Homo sapiens, Xenopus tropicalis, Mus musculus
D214TDFHIDFGGTS1Drosophila melanogaster
H212CYTDFHVDFGG3Homo sapiens, Xenopus tropicalis, Mus musculus
H212CYTDFHIDFGG1Drosophila melanogaster
H284PSGWIHAVYTP3Homo sapiens, Xenopus tropicalis, Mus musculus
H284PTGWIHAVYTP1Drosophila melanogaster
H650CNEIVHPGCL-3Homo sapiens, Xenopus tropicalis, Mus musculus
H650CYEIAHPDCAL1Drosophila melanogaster
I144KLYNVISLEFS3Homo sapiens, Xenopus tropicalis, Mus musculus
I144-LLNVISLEFS1Drosophila melanogaster
K229IHQGGKVFWLI2Homo sapiens, Mus musculus
K229ILRGSKVFWLI1Drosophila melanogaster
K229ILRGGKVFWLI1Xenopus tropicalis
N142REKLYNVISLE3Homo sapiens, Xenopus tropicalis, Mus musculus
N142R--LLNVISLE1Drosophila melanogaster
T209VRGCYTDFHVD3Homo sapiens, Xenopus tropicalis, Mus musculus
T209VKNCYTDFHID1Drosophila melanogaster
V286GWIHAVYTPTD2Homo sapiens, Mus musculus
V286GWIHAVYTPTQ1Drosophila melanogaster
V286GWIHAVYTPQD1Xenopus tropicalis
Y222GTSVWYHIHQG2Homo sapiens, Mus musculus
Y222GTSVWYHILRG2Drosophila melanogaster, Xenopus tropicalis

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