title: Identifying N6-methyladenosine sites in the Arabidopsis thaliana transcriptome.
abstract: N6-Methyladenosine (m6A) plays important roles in many biological processes. The knowledge of the distribution of m6A is helpful for understanding its regulatory roles. Although the experimental methods have been proposed to detect m6A, the resolutions of these methods are still unsatisfying especially for Arabidopsis thaliana. Benefitting from the experimental data, in the current work, a support vector machine-based method was proposed to identify m6A sites in A. thaliana transcriptome. The proposed method was validated on a benchmark dataset using jackknife test and was also validated by identifying strain-specific m6A sites in A. thaliana. The obtained predictive results indicate that the proposed method is quite promising. For the convenience of experimental biologists, an online webserver for the proposed method was built, which is freely available at http://lin.uestc.edu.cn/server/M6ATH . These results indicate that the proposed method holds a potential to become an elegant tool in identifying m6A site in A. thaliana.
authors: Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, China. chenweiimu@gmail.com.
authors: Wei
authors: W
authors: Chen
authors: School of Public Health, North China University of Science and Technology, Tangshan, 063000, China.
authors: Pengmian
authors: P
authors: Feng
authors: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics and Center for Information in Biomedicine, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
authors: Hui
authors: H
authors: Ding
authors: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics and Center for Information in Biomedicine, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China. hlin@uestc.edu.cn.
authors: Hao
authors: H
authors: Lin
mesh_terms: D000241:Adenosine / Q000031:analogs & derivatives* / Q000378:metabolism; D017360:Arabidopsis / Q000737:chemistry / Q000235:genetics*; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D018749:RNA, Plant / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D060388:Support Vector Machine; D059467:Transcriptome
chemical_list: D018749:RNA, Plant; C010223:N-methyladenosine; D000241:Adenosine
keywords: Chemical functionality; Hydrogen bond; Ring structure; Support vector machine; m6A