SynLethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery

Abstract

Abstract Two genes are synthetic lethal if mutations in both genes result in impaired cell viability, while mutation of either gene does not affect the cell survival. The potential usage of synthetic lethality (SL) in anticancer therapeutics has attracted many researchers to identify synthetic lethal gene pairs. To include newly identified SLs and more related knowledge, we present a new version of the SynLethDB database to facilitate the discovery of clinically relevant SLs. We extended the first version of SynLethDB database significantly by including new SLs identified through Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) screening, a knowledge graph about human SLs, a new web interface, etc. Over 16 000 new SLs and 26 types of other relationships have been added, encompassing relationships among 14 100 genes, 53 cancers, 1898 drugs, etc. Moreover, a brand-new web interface has been developed to include modules such as SL query by disease or compound, SL partner gene set enrichment analysis and knowledge graph browsing through a dynamic graph viewer. The data can be downloaded directly from the website or through the RESTful Application Programming Interfaces (APIs). Database URL:  https://synlethdb.sist.shanghaitech.edu.cn/v2.