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

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-consumi...

Full description

Saved in:
Bibliographic Details
Published in:Briefings in bioinformatics 2020-01, Vol.21 (1), p.171-181
Main Authors: Dong, Chuan, Jin, Yan-Ting, Hua, Hong-Li, Wen, Qing-Feng, Luo, Sen, Zheng, Wen-Xin, Guo, Feng-Biao
Format: Article
Language:English
Subjects:
Computer applications
Conserved sequence
E coli
Eukaryotes
Evolutionary conservation
Genes
Identification methods
Network topologies
Prokaryotes
Topology
Citations: Items that this one cites
Items that cite this one
Online Access:Request full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/bby116