title: SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets.
abstract: Synthetic lethality (SL) is a type of genetic interaction between two genes such that simultaneous perturbations of the two genes result in cell death or a dramatic decrease of cell viability, while a perturbation of either gene alone is not lethal. SL reflects the biologically endogenous difference between cancer cells and normal cells, and thus the inhibition of SL partners of genes with cancer-specific mutations could selectively kill cancer cells but spare normal cells. Therefore, SL is emerging as a promising anticancer strategy that could potentially overcome the drawbacks of traditional chemotherapies by reducing severe side effects. Researchers have developed experimental technologies and computational prediction methods to identify SL gene pairs on human and a few model species. However, there has not been a comprehensive database dedicated to collecting SL pairs and related knowledge. In this paper, we propose a comprehensive database, SynLethDB (http://histone.sce.ntu.edu.sg/SynLethDB/), which contains SL pairs collected from biochemical assays, other related databases, computational predictions and text mining results on human and four model species, i.e. mouse, fruit fly, worm and yeast. For each SL pair, a confidence score was calculated by integrating individual scores derived from different evidence sources. We also developed a statistical analysis module to estimate the druggability and sensitivity of cancer cells upon drug treatments targeting human SL partners, based on large-scale genomic data, gene expression profiles and drug sensitivity profiles on more than 1000 cancer cell lines. To help users access and mine the wealth of the data, we developed other practical functionalities, such as search and filtering, orthology search, gene set enrichment analysis. Furthermore, a user-friendly web interface has been implemented to facilitate data analysis and interpretation. With the integrated data sets and analytics functionalities, SynLethDB would be a useful resource for biomedical research community and pharmaceutical industry.
authors.affiliation: School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore.
authors.forename: Jing
authors.initials: J
authors.lastname: Guo
authors.affiliation: School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore Lab of Information Management, Changzhou University, Jiangsu 213164, China hliu@cczu.edu.cn.
authors.forename: Hui
authors.initials: H
authors.lastname: Liu
authors.affiliation: School of Computer Engineering, Nanyang Technological University, Singapore 639798, Singapore Genome Institute of Singapore (GIS), Biopolis, Singapore 138672, Singapore ZhengJie@ntu.edu.sg.
authors.forename: Jie
authors.initials: J
authors.lastname: Zheng
mesh_terms: D000818:Animals; D000970:Antineoplastic Agents / Q000494:pharmacology*; D016923:Cell Death; D045744:Cell Line, Tumor; D003627:Data Interpretation, Statistical; D062313:Databases, Pharmaceutical; D055808:Drug Discovery; D052138:Genes, Neoplasm; D006801:Humans; D051379:Mice; D009154:Mutation; D034622:RNA Interference
chemical_list: D000970:Antineoplastic Agents