Wen-Xin Zheng*, Shu-Xuan Wang and Hong Liu
Background: Many studies have been conducted on essentiality prediction in the Saccharomyces cerevisiae genome, but the accuracy is not as high as those in bacterial or human genomes. The most frequently used features are protein-protein interaction (PPI) networks combined with some other features, such as evolutionary conservation, expression level, and protein domain information. Sequence composition features are used least often.
Objective: To improve the accuracy of essentiality prediction in the Saccharomyces cerevisiae genome, we proposed a highly accurate gene essentiality prediction algorithm.
Methods: In this paper, we propose an algorithm based on a linear support vector machine (SVM) using sequence features only. The variables in this paper are derived from sequence data based on the w-nucleotide Z curve format without any other information.
Results: After feature selection, the best area under the receiver operating characteristic curve (AUC) was 0.944 for 5-fold cross-validation. From 1- to 6-nucleotide Z curve variables, feature extraction can increase the AUC in all cases.
Conclusion: Prediction only on sequence composition is promising, particularly when a feature filtering method is used, and maybe a good complement for algorithms based on other features.
Essential gene prediction, Sequence composition, The w-nucleotide Z curve, Saccharomyces cerevisiae.
School of Biomedical Engineering, Capital Medical University, Beijing 100069, , School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, , Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing 100069