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mutLBSgeneDB |
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| Gene summary for KDM4B |
 Gene summary |
| Basic gene Info. | Gene symbol | KDM4B |
| Gene name | lysine (K)-specific demethylase 4B | |
| Synonyms | JMJD2B|TDRD14B | |
| Cytomap | UCSC genome browser: 19p13.3 | |
| Type of gene | protein-coding | |
| RefGenes | NM_015015.2, | |
| Description | jmjC domain-containing histone demethylation protein 3Bjumonji domain containing 2Bjumonji domain-containing protein 2Blysine-specific demethylase 4Btudor domain containing 14B | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 609765 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000127663 | ||
| HPRD : 11056 | ||
| Vega : OTTHUMG00000180281 | ||
| Protein | UniProt: O94953 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_KDM4B | |
| BioGPS: 23030 | ||
| Pathway | NCI Pathway Interaction Database: KDM4B | |
| KEGG: KDM4B | ||
| REACTOME: KDM4B | ||
| Pathway Commons: KDM4B | ||
| Context | iHOP: KDM4B | |
| ligand binding site mutation search in PubMed: KDM4B | ||
| UCL Cancer Institute: KDM4B | ||
| Assigned class in mutLBSgeneDB | C: This gene just belongs to 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 KDM4B |
| 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 | E191 | E191K | STAD | 1 | Y133 | P131L | UCEC | 1 | C235 | A237T | UCEC | 1 | M243 | M243I | UCEC | 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 KDM4B |
| 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 | Y133 | P131L | 0.10150674 | E191 | E191K | -0.94223048 | C235 | A237T | -0.33911879 | M243 | M243I | -0.33399362 |
| (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 KDM4B from PDB |
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| Differential gene expression and gene-gene network for KDM4B |
| 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 KDM4B |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0025149 | Medulloblastoma | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for KDM4B |
| 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 KDM4B go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ZN | ZINC(2+) | 4lxl | A | C235 | III | Peptide ligand (ALA,ARG,LYS,SER,THR,GLY,GLY,LYS) | 4lxl | A | E191 M243 | PD2 | LUTIDINIC ACID | 4lxl | A | Y133 E191 |
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| Conservation information for LBS of KDM4B |
| Multiple alignments for O94953 in multiple species |
| LBS | AA sequence | # species | Species |
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