title: Prediction of human disease-associated phosphorylation sites with combined feature selection approach and support vector machine.
abstract: Phosphorylation is a crucial post-translational modification, which regulates almost all cellular processes in life. It has long been recognised that protein phosphorylation has close relationship with diseases, and therefore many researches are undertaken to predict phosphorylation sites for disease treatment and drug design. However, despite the success achieved by these approaches, no method focuses on disease-associated phosphorylation sites prediction. Herein, for the first time the authors propose a novel approach that is specially designed to identify associations between phosphorylation sites and human diseases. To take full advantage of local sequence information, a combined feature selection method-based support vector machine (CFS-SVM) that incorporates minimum-redundancy-maximum-relevance filtering process and forward feature selection process is developed. Performance evaluation shows that CFS-SVM is significantly better than the widely used classifiers including Bayesian decision theory, k nearest neighbour and random forest. With the extremely high specificity of 99%, CFS-SVM can still achieve a high sensitivity. Besides, tests on extra data confirm the effectiveness and general applicability of CFS-SVM approach on a variety of diseases. Finally, the analysis of selected features and corresponding kinases also help the understanding of the potential mechanism of disease-phosphorylation relationships and guide further experimental validations.
authors.affiliation: School of Information Science and Technology, University of Science and Technology of China, Hefei AH230027, People's Republic of China.
authors.forename: Xiaoyi
authors.initials: X
authors.lastname: Xu
authors.affiliation: Centers for Biomedical Engineering, University of Science and Technology of China, Hefei AH230027, People's Republic of China.
authors.forename: Ao
authors.initials: A
authors.lastname: Li
authors.affiliation: Centers for Biomedical Engineering, University of Science and Technology of China, Hefei AH230027, People's Republic of China. mhwang@ustc.edu.cn.
authors.forename: Minghui
authors.initials: M
authors.lastname: Wang
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D004198:Disease Susceptibility / Q000175:diagnosis / Q000378:metabolism*; D006801:Humans; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods; D010770:Phosphotransferases / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D020543:Proteome / Q000737:chemistry* / Q000378:metabolism*; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*; D060388:Support Vector Machine
chemical_list: D020543:Proteome; D010770:Phosphotransferases