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mutLBSgeneDB |
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| Gene summary for KDM2A |
 Gene summary |
| Basic gene Info. | Gene symbol | KDM2A |
| Gene name | lysine (K)-specific demethylase 2A | |
| Synonyms | CXXC8|FBL11|FBL7|FBXL11|JHDM1A|LILINA | |
| Cytomap | UCSC genome browser: 11q13.2 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001256405.1, NM_012308.2,NR_027473.1, | |
| Description | CXXC-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 date | 20141207 | |
| dbXrefs | MIM : 605657 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000173120 | ||
| HPRD : 05741 | ||
| Vega : OTTHUMG00000167103 | ||
| Protein | UniProt: Q9Y2K7 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_KDM2A | |
| BioGPS: 22992 | ||
| Pathway | NCI Pathway Interaction Database: KDM2A | |
| KEGG: KDM2A | ||
| REACTOME: KDM2A | ||
| Pathway Commons: KDM2A | ||
| Context | iHOP: KDM2A | |
| ligand binding site mutation search in PubMed: KDM2A | ||
| UCL Cancer Institute: KDM2A | ||
| Assigned class in mutLBSgeneDB | B: This gene belongs to targetable_mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID |
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| 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. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | Y222 | H223R | COAD | 1 | Y222 | W221L | LUSC | 1 | Y222 | H223Y | OV | 1 |
| 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 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 |
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| 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. |
| LBS | AAchange of nsSNV | Relative stability change | Y222 | W221L | -1.1165372 | Y222 | H223Y | -0.373891 | Y222 | H223R | -0.36499847 |
| (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 |
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| 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) |
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| Phenotype information for KDM2A |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| 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. |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of KDM2A go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | AKG | 2-OXOGLUTARIC ACID | 2yu1 | A | Y222 |
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| Conservation information for LBS of KDM2A |
| Multiple alignments for Q9Y2K7 in multiple species |
| LBS | AA sequence | # species | Species | C582 | CVQGECGVCHY | 2 | Homo sapiens, Mus musculus | C582 | CQRSDCGTCPF | 1 | Drosophila melanogaster | C582 | CVQRECGTCHY | 1 | Xenopus tropicalis | C585 | GECGVCHYCRD | 2 | Homo sapiens, Mus musculus | C585 | SDCGTCPFCMD | 1 | Drosophila melanogaster | C585 | RECGTCHYCKD | 1 | Xenopus tropicalis | C588 | GVCHYCRDMKK | 2 | Homo sapiens, Mus musculus | C588 | GTCPFCMDMVK | 1 | Drosophila melanogaster | C588 | GTCHYCKDMKK | 1 | Xenopus tropicalis | C604 | RMKQSCVLRQC | 3 | Homo sapiens, Xenopus tropicalis, Mus musculus | C604 | RAKQTCMMRQC | 1 | Drosophila melanogaster | C620 | PHSVTCSLC-- | 2 | Homo sapiens, Mus musculus | C620 | PVTAQCVYCHL | 1 | Drosophila melanogaster | C620 | PHSVTCALC-- | 1 | Xenopus tropicalis | C623 | VTCSLC----- | 2 | Homo sapiens, Mus musculus | C623 | AQCVYCHLDGW | 1 | Drosophila melanogaster | C623 | VTCALC----- | 1 | Xenopus tropicalis | C653 | IVHPGCL--QM | 2 | Homo sapiens, Mus musculus | C653 | IAHPDCALSQL | 1 | Drosophila melanogaster | C653 | IVHPGCL--EM | 1 | Xenopus tropicalis | D214 | TDFHVDFGGTS | 3 | Homo sapiens, Xenopus tropicalis, Mus musculus | D214 | TDFHIDFGGTS | 1 | Drosophila melanogaster | H212 | CYTDFHVDFGG | 3 | Homo sapiens, Xenopus tropicalis, Mus musculus | H212 | CYTDFHIDFGG | 1 | Drosophila melanogaster | H284 | PSGWIHAVYTP | 3 | Homo sapiens, Xenopus tropicalis, Mus musculus | H284 | PTGWIHAVYTP | 1 | Drosophila melanogaster | H650 | CNEIVHPGCL- | 3 | Homo sapiens, Xenopus tropicalis, Mus musculus | H650 | CYEIAHPDCAL | 1 | Drosophila melanogaster | I144 | KLYNVISLEFS | 3 | Homo sapiens, Xenopus tropicalis, Mus musculus | I144 | -LLNVISLEFS | 1 | Drosophila melanogaster | K229 | IHQGGKVFWLI | 2 | Homo sapiens, Mus musculus | K229 | ILRGSKVFWLI | 1 | Drosophila melanogaster | K229 | ILRGGKVFWLI | 1 | Xenopus tropicalis | N142 | REKLYNVISLE | 3 | Homo sapiens, Xenopus tropicalis, Mus musculus | N142 | R--LLNVISLE | 1 | Drosophila melanogaster | T209 | VRGCYTDFHVD | 3 | Homo sapiens, Xenopus tropicalis, Mus musculus | T209 | VKNCYTDFHID | 1 | Drosophila melanogaster | V286 | GWIHAVYTPTD | 2 | Homo sapiens, Mus musculus | V286 | GWIHAVYTPTQ | 1 | Drosophila melanogaster | V286 | GWIHAVYTPQD | 1 | Xenopus tropicalis | Y222 | GTSVWYHIHQG | 2 | Homo sapiens, Mus musculus | Y222 | GTSVWYHILRG | 2 | Drosophila melanogaster, Xenopus tropicalis |
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