title: Prediction of CpG island methylation status by integrating DNA physicochemical properties.
abstract: As an inheritable epigenetic modification, DNA methylation plays important roles in many biological processes. The non-uniform distribution of DNA methylation across the genome implies that characterizing genome-wide DNA methylation patterns is necessary to better understand the regulatory mechanisms of DNA methylation. Although a series of experimental technologies have been proposed, they are cost-ineffective for DNA methylation status detection. As complements to experimental techniques, computational methods will facilitate the identification of DNA methylation status. In the present study, we proposed a Naïve Bayes model to predict CpG island methylation status. In this model, DNA sequences are formulated by "pseudo trinucleotide composition" into which three DNA physicochemical properties were incorporated. It was observed by the jack-knife test that the overall success rate achieved by the proposed model in predicting the DNA methylation status was 88.22%. This result indicates that the proposed model is a useful tool for DNA methylation status prediction.
authors.affiliation: School of Public Health, Hebei United University, Tangshan, 063000, China. Electronic address: fengpengmian@gmail.com.
authors.forename: Pengmian
authors.initials: P
authors.lastname: Feng
authors.affiliation: Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China. Electronic address: greatchen@heuu.edu.cn.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China. Electronic address: hlin@uestc.edu.cn.
authors.forename: Hao
authors.initials: H
authors.lastname: Lin
mesh_terms: D001499:Bayes Theorem; D018899:CpG Islands; D004247:DNA / Q000737:chemistry*; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D015894:Genome, Human; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA
keywords: CpG island; DNA methylation; DNA physicochemical property; Naïve Bayes; Pseudo trinucleotide composition