Dong Chuan, Jin Yan-Ting, Hua Hong-Li, Wen Qing-Feng, Luo Sen, Zheng Wen-Xin, Guo Feng-Biao
School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
School of Biomedical Engineering, Capital Medical University, Beijing, China.
Brief Bioinform. 2020 Jan 17;21(1):171-181. doi: 10.1093/bib/bby116.
Essential genes have attracted increasing attention in recent years due to the important functions of these genes in organisms. Among the methods used to identify the essential genes, accurate and efficient computational methods can make up for the deficiencies of expensive and time-consuming experimental technologies. In this review, we have collected researches on essential gene predictions in prokaryotes and eukaryotes and summarized the five predominant types of features used in these studies. The five types of features include evolutionary conservation, domain information, network topology, sequence component and expression level. We have described how to implement the useful forms of these features and evaluated their performance based on the data of Escherichia coli MG1655, Bacillus subtilis 168 and human. The prerequisite and applicable range of these features is described. In addition, we have investigated the techniques used to weight features in various models. To facilitate researchers in the field, two available online tools, which are accessible for free and can be directly used to predict gene essentiality in prokaryotes and humans, were referred. This article provides a simple guide for the identification of essential genes in prokaryotes and eukaryotes.
近年来，必需基因因其在生物体中的重要功能而受到越来越多的关注。在用于鉴定必需基因的方法中，准确且高效的计算方法可以弥补昂贵且耗时的实验技术的不足。在本综述中，我们收集了关于原核生物和真核生物中必需基因预测的研究，并总结了这些研究中使用的五种主要特征类型。这五种特征类型包括进化保守性、结构域信息、网络拓扑结构、序列组成和表达水平。我们描述了如何实现这些特征的有用形式，并基于大肠杆菌MG1655、枯草芽孢杆菌168和人类的数据评估了它们的性能。描述了这些特征的前提条件和适用范围。此外，我们研究了在各种模型中用于对特征进行加权的技术。为方便该领域的研究人员，文中提及了两个免费在线工具，可直接用于预测原核生物和人类中的基因必需性。本文为鉴定原核生物和真核生物中的必需基因提供了一个简要指南。
