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mutLBSgeneDB |
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| Gene summary for MBD4 |
 Gene summary |
| Basic gene Info. | Gene symbol | MBD4 |
| Gene name | methyl-CpG binding domain protein 4 | |
| Synonyms | MED1 | |
| Cytomap | UCSC genome browser: 3q21.3 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001276270.1, NM_001276271.1,NM_001276272.1,NM_001276273.1,NM_003925.2, | |
| Description | 3,N(4)-ethenocytosine glycosylaseG/5-fluorouracil mismatch glycosylase with biphasic kineticsG/T mismatch glycosylaseG/U mismatch glycosylasemethyl-CpG-binding domain protein 4methyl-CpG-binding endonuclease 1methyl-CpG-binding protein MBD4mismatch | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 603574 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000129071 | ||
| HPRD : 04654 | ||
| Vega : OTTHUMG00000159463 | ||
| Protein | UniProt: O95243 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_MBD4 | |
| BioGPS: 8930 | ||
| Pathway | NCI Pathway Interaction Database: MBD4 | |
| KEGG: MBD4 | ||
| REACTOME: MBD4 | ||
| Pathway Commons: MBD4 | ||
| Context | iHOP: MBD4 | |
| ligand binding site mutation search in PubMed: MBD4 | ||
| UCL Cancer Institute: MBD4 | ||
| 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 MBD4 |
| 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 | G507 | G507S | COAD | 2 | L511 | R512W | COAD | 1 | M473 | M473I | COAD | 1 | L506 | L506V | LUAD | 1 | K117 | K117R | STAD | 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 MBD4 |
| 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 | G507 | G507S | -1.0927953 | L511 | R512W | -1.0773541 | L506 | L506V | -0.61832042 | K117 | K117R | -0.30807438 | M473 | M473I | -0.069543448 |
| (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 MBD4 from PDB |
| PDB ID | PDB title | PDB structure | 3IHO | The C-terminal glycosylase domain of human MBD4 |  |
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| Differential gene expression and gene-gene network for MBD4 |
| 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 MBD4 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0004352 | Autistic Disorder | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for MBD4 |
| 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 MBD4 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | NUC | Nucleic Acids | 2moe | A | K117 | NUC | Nucleic Acids | 4e9f | A | L511 | NUC | Nucleic Acids | 4e9g | A | L511 | NUC | Nucleic Acids | 4e9h | A | L511 | NUC | Nucleic Acids | 4ea4 | A | L511 | NUC | Nucleic Acids | 4ofa | A | L511 | NUC | Nucleic Acids | 4ofe | A | L511 | NUC | Nucleic Acids | 4ofh | A | L511 | NUC | Nucleic Acids | 4dk9 | A | M473 L506 G507 L511 | NUC | Nucleic Acids | 4e9f | A | M473 L506 G507 L511 | NUC | Nucleic Acids | 4e9g | A | M473 L506 G507 L511 | NUC | Nucleic Acids | 4e9h | A | M473 L506 G507 L511 | NUC | Nucleic Acids | 4ea4 | A | M473 L506 G507 L511 | NUC | Nucleic Acids | 4ea5 | A | M473 L506 G507 L511 | NUC | Nucleic Acids | 4ofa | A | M473 L506 G507 L511 | NUC | Nucleic Acids | 4ofe | A | M473 L506 G507 L511 | NUC | Nucleic Acids | 4ofh | A | M473 L506 G507 L511 |
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| Conservation information for LBS of MBD4 |
| Multiple alignments for O95243 in multiple species |
| LBS | AA sequence | # species | Species |
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