title: PGlcS: Prediction of protein O-GlcNAcylation sites with multiple features and analysis.
abstract: As a widespread type of protein post-translational modification, O-GlcNAcylation plays crucial regulatory roles in almost all cellular processes and is related to some diseases. To deeply understand O-GlcNAcylated mechanisms, identification of substrates and specific O-GlcNAcylated sites is crucial. Experimental identification is expensive and time-consuming, so computational prediction of O-GlcNAcylated sites has considerable value. In this work, we developed a novel O-GlcNAcylated sites predictor called PGlcS (Prediction of O-GlcNAcylated Sites) by using k-means cluster to obtain informative and reliable negative samples, and support vector machines classifier combined with a two-step feature selection. The performance of PGlcS was evaluated using an independent testing dataset resulting in a sensitivity of 64.62%, a specificity of 68.4%, an accuracy of 68.37%, and a Matthew׳s correlation coefficient of 0.0697, which demonstrated PGlcS was very promising for predicting O-GlcNAcylated sites. The datasets and source code were available in Supplementary information.
authors.affiliation: School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China. Electronic address: zhaoxw303@nenu.edu.cn.
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Zhao
authors.affiliation: School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China.
authors.forename: Qiao
authors.initials: Q
authors.lastname: Ning
authors.affiliation: School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China.
authors.forename: Haiting
authors.initials: H
authors.lastname: Chai
authors.affiliation: School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China.
authors.forename: Meiyue
authors.initials: M
authors.lastname: Ai
authors.affiliation: School of Computer Science and Information Technology, Northeast Normal University, Changchun 130117, China.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Ma
mesh_terms: D000117:Acetylglucosamine / Q000378:metabolism*; D000215:Acylation; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000378:metabolism*
chemical_list: D011506:Proteins; D000117:Acetylglucosamine
keywords: A two-step feature selection; O-GlcNAcylated mechanisms; Support vector machines; k-means cluster