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mutLBSgeneDB |
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| Gene summary for TOPBP1 |
 Gene summary |
| Basic gene Info. | Gene symbol | TOPBP1 |
| Gene name | topoisomerase (DNA) II binding protein 1 | |
| Synonyms | TOP2BP1 | |
| Cytomap | UCSC genome browser: 3q22.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_007027.3, | |
| Description | DNA topoisomerase 2-binding protein 1DNA topoisomerase II-beta-binding protein 1DNA topoisomerase II-binding protein 1 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 607760 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000163781 | ||
| HPRD : 09678 | ||
| Vega : OTTHUMG00000159773 | ||
| Protein | UniProt: Q92547 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_TOPBP1 | |
| BioGPS: 11073 | ||
| Pathway | NCI Pathway Interaction Database: TOPBP1 | |
| KEGG: TOPBP1 | ||
| REACTOME: TOPBP1 | ||
| Pathway Commons: TOPBP1 | ||
| Context | iHOP: TOPBP1 | |
| ligand binding site mutation search in PubMed: TOPBP1 | ||
| UCL Cancer Institute: TOPBP1 | ||
| 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 | GO:0006974 | cellular response to DNA damage stimulus | 12773567 | GO:0010212 | response to ionizing radiation | 12773567 |
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| Ligand binding site mutations for TOPBP1 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | Q655 | A657G | COAD | 1 | T1466 | L1464F | HNSC | 1 | E1467 | Y1468C | STAD | 1 | A707 | A708E | THCA | 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 TOPBP1 |
| 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 | T1466 | L1464F | -1.3160855 | E1467 | Y1468C | -1.2167206 | A707 | A708E | -0.95031519 | Q655 | A657G | -0.45170726 |
| (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 TOPBP1 from PDB |
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| Differential gene expression and gene-gene network for TOPBP1 |
| 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 TOPBP1 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0023434 | Leukemia, Lymphocytic, Chronic, B-Cell | 1 | Biomarker, GeneticVariation |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for TOPBP1 |
| 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 TOPBP1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | III | Peptide ligand (PHE,ILE,ASP,SER,ASP,THR,ASP,VAL,GLU,GLU) | 3ueo | B | Q655 | III | Peptide ligand (ASP,SER,ASP,THR,ASP,VAL,GLU,GLU) | 3ueo | C | Q655 A707 | III | Peptide ligand (PHE,ILE,ASP,SER,ASP,THR,ASP,VAL,GLU,GLU) | 3ueo | D | Q655 A707 | III | Peptide ligand (SER,ILE,TYR,PHE,THR,PRO,GLU,LEU,TYR,ASP) | 3al3 | A | T1466 E1467 |
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| Conservation information for LBS of TOPBP1 |
| Multiple alignments for Q92547 in multiple species |
| LBS | AA sequence | # species | Species |
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