title: A method to distinguish between lysine acetylation and lysine ubiquitination with feature selection and analysis.
abstract: Lysine acetylation and ubiquitination are two primary post-translational modifications (PTMs) in most eukaryotic proteins. Lysine residues are targets for both types of PTMs, resulting in different cellular roles. With the increasing availability of protein sequences and PTM data, it is challenging to distinguish the two types of PTMs on lysine residues. Experimental approaches are often laborious and time consuming. There is an urgent need for computational tools to distinguish between lysine acetylation and ubiquitination. In this study, we developed a novel method, called DAUFSA (distinguish between lysine acetylation and lysine ubiquitination with feature selection and analysis), to discriminate ubiquitinated and acetylated lysine residues. The method incorporated several types of features: PSSM (position-specific scoring matrix) conservation scores, amino acid factors, secondary structures, solvent accessibilities, and disorder scores. By using the mRMR (maximum relevance minimum redundancy) method and the IFS (incremental feature selection) method, an optimal feature set containing 290 features was selected from all incorporated features. A dagging-based classifier constructed by the optimal features achieved a classification accuracy of 69.53%, with an MCC of .3853. An optimal feature set analysis showed that the PSSM conservation score features and the amino acid factor features were the most important attributes, suggesting differences between acetylation and ubiquitination. Our study results also supported previous findings that different motifs were employed by acetylation and ubiquitination. The feature differences between the two modifications revealed in this study are worthy of experimental validation and further investigation.
authors.affiliation: a The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine , Shanghai 200031 , P.R. China.
authors.forename: You
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: b Department of Biomedical Engineering, Tianjin Key Lab of BME Measurement , Tianjin University , Tianjin 300072 , P.R. China.
authors.forename: Ning
authors.initials: N
authors.lastname: Zhang
authors.affiliation: c Key Laboratory of Systems Biology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200031 , P.R. China.
authors.forename: Bi-Qing
authors.initials: BQ
authors.lastname: Li
authors.affiliation: a The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine , Shanghai 200031 , P.R. China.|d Department of Genetics and Genomic Sciences , Icahn School of Medicine at Mount Sinai , New York , NY 10029 , USA.
authors.forename: Tao
authors.initials: T
authors.lastname: Huang
authors.affiliation: e Institute of Systems Biology , Shanghai University , Shanghai 200444 , P.R. China.
authors.forename: Yu-Dong
authors.initials: YD
authors.lastname: Cai
authors.affiliation: a The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine , Shanghai 200031 , P.R. China.
authors.forename: Xiang-Yin
authors.initials: XY
authors.lastname: Kong
mesh_terms: D000107:Acetylation; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence; D030541:Databases, Genetic; D008239:Lysine / Q000737:chemistry* / Q000378:metabolism*; D056510:Position-Specific Scoring Matrices; D011487:Protein Conformation; D011499:Protein Processing, Post-Translational; D054875:Ubiquitination
chemical_list: D008239:Lysine
keywords: acetylation; dagging; incremental feature selection; post-translational modification; ubiquitination