Comprehensive review of the identification of essential genes using computational methods: focusing on feature implementation and assessment

Chuan Dong; Yan-Ting Jin; Hong-Li Hua; Qing-Feng Wen; Sen Luo; Wen-Xin Zheng; Feng-Biao Guo

doi:10.1093/bib/bby116

Comprehensive review of the identification of essential genes using computational methods: focusing on feature implementation and assessment

Brief Bioinform. 2020 Jan 17;21(1):171-181. doi: 10.1093/bib/bby116.

Authors

Chuan Dong¹, Yan-Ting Jin¹, Hong-Li Hua¹, Qing-Feng Wen¹, Sen Luo¹, Wen-Xin Zheng², Feng-Biao Guo³

Affiliations

¹ School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
² School of Biomedical Engineering, Capital Medical University, Beijing, China.
³ School of Life Science and Technology, Center for Informational Biology, Intelligent Learning Institute for Science and Application, University of Electronic Science and Technology of China, Chengdu, China.

PMID: 30496347
DOI: 10.1093/bib/bby116

Abstract

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.

Keywords: computational methods; essential genes; feature assessment; online tool.