A new computational strategy for predicting essential genes

• Published in: BMC genomics Vol. 14; no. 1; p. 910
• Main Authors: Cheng, Jian, Wu, Wenwu, Zhang, Yinwen, Li, Xiangchen, Jiang, Xiaoqian, Wei, Gehong, Tao, Shiheng
• Format: Journal Article
• Language: English
• Published: London BioMed Central 21.12.2013; BioMed Central Ltd; Springer Nature B.V
• Subjects: Algorithms; Analysis; Animal Genetics and Genomics; Bayes Theorem; Biomedical and Life Sciences; Computational Biology - methods; Eukaryote microbial genomics; Genes; Genes, Essential; Genetic vectors; Genomes; Genomics; Life Sciences; Logistic Models; Methodology; Methodology Article; Microarrays; Microbial Genetics and Genomics; Microorganisms; Models, Genetic; Mutagenesis; Organisms; Plant Genetics and Genomics; Prediction models; Proteomics; Studies; Support Vector Machine; Iran; Taiwan; Essential genes; Naïve Bayes; Support vector machine; Gene essentiality
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/1471-2164-14-910

Background Determination of the minimum gene set for cellular life is one of the central goals in biology. Genome-wide essential gene identification has progressed rapidly in certain bacterial species; however, it remains difficult to achieve in most eukaryotic species. Several computational models have recently been developed to integrate gene features and used as alternatives to transfer gene essentiality annotations between organisms. Results We first collected features that were widely used by previous predictive models and assessed the relationships between gene features and gene essentiality using a stepwise regression model. We found two issues that could significantly reduce model accuracy: (i) the effect of multicollinearity among gene features and (ii) the diverse and even contrasting correlations between gene features and gene essentiality existing within and among different species. To address these issues, we developed a novel model called feature-based weighted Naïve Bayes model (FWM), which is based on Naïve Bayes classifiers, logistic regression, and genetic algorithm. The proposed model assesses features and filters out the effects of multicollinearity and diversity. The performance of FWM was compared with other popular models, such as support vector machine, Naïve Bayes model, and logistic regression model, by applying FWM to reciprocally predict essential genes among and within 21 species. Our results showed that FWM significantly improves the accuracy and robustness of essential gene prediction. Conclusions FWM can remarkably improve the accuracy of essential gene prediction and may be used as an alternative method for other classification work. This method can contribute substantially to the knowledge of the minimum gene sets required for living organisms and the discovery of new drug targets.