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Computational Method for Distinguishing Lysine Acetylation, Sumoylation, and Ubiquitination using the Random Forest Algorithm with a Feature Selection Procedure

文献类型：期刊论文

作者Wang, ShaoPeng1; Li, JiaRui1; Cai, Yu-Dong1; Yuan, Fei2; Chen, Lei3; Huang, Tao4; ,
刊名COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING
出版日期2017
卷号20期号:10页码:886-895
关键词Post-translational modification acetylation sumoylation ubiquitination maximum relevance minimum redundancy random forest disordered region in protein
ISSN号1386-2073
DOI10.2174/1386207321666171218114056
文献子类Article
英文摘要Background: The post-translational modifications (PTMs) on the side chains of conserved lysine (Lys) residues play important roles in myriad cellular processes, such as modification of the structures and activities of histones, protein degradation and turnover, and the regulation of DNA damage responses. To date, several computational methods have been developed to identify different PTMs on Lys residues. However, most of these methods focused on identifying one particular PTM regardless of other types of PTMs. Method: In this study, we first conducted a computational investigation of three types of PTMs (acetylation, sumoylation, and ubiquitination) at the same time by analyzing the protein structure and sequence factors surrounding the substrate Lysresidues in these types of PTMs. To fully extract the structural and sequence information around the Lysresidues, six types of features were used to encode the peptide segments containing the substrates. Next, through a feature selection method, i.e., maximum relevance minimum redundancy (mRMR), two feature lists, i.e., MaxRel feature list and mRMR feature list, were obtained. For the mRMR feature list, it was applied to extract the optimal features of the random forest algorithm for distinguishing three types of PTMs. Results: An optimal classification model with an overall accuracy of 0.989 was built. For the MaxRel feature list, we investigated the top-ranked features to uncover the site-preference and residue-preference of Lys residues. Conclusion: The results suggested that the disorder structure and the preference of flanking residues were the most important attributes to distinguish the three types of PTMs, which were consistent with the results reported in previous studies.
学科主题Biochemistry & Molecular Biology ; Chemistry ; Pharmacology & Pharmacy
WOS关键词PHOSPHORYLATION-DEPENDENT SUMOYLATION ; HISTONE ACETYLTRANSFERASE COMPLEXES ; REDUNDANCY MAXIMUM RELEVANCE ; INTRINSIC DISORDER ; POSTTRANSLATIONAL MODIFICATIONS ; UNSTRUCTURED PROTEINS ; GENE ONTOLOGY ; SUMO ; PREDICTION ; SITES
语种英语
WOS记录号WOS:000425051500007
出版者BENTHAM SCIENCE PUBL LTD
版本出版稿
源URL[http://202.127.25.144/handle/331004/1160]  
专题中国科学院上海生命科学研究院营养科学研究所
作者单位1.Shanghai Univ, Coll Life Sci, Shanghai 200444, Peoples R China;
2.Binzhou Med Univ Hosp, Dept Sci & Technol, Binzhou 256603, Shandong, Peoples R China;
3.Shanghai Maritime Univ, Coll Informat Engn, Shanghai 201306, Peoples R China;
4.Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Hlth Sci, Shanghai 200031, Peoples R China,
推荐引用方式
GB/T 7714		 Wang, ShaoPeng,Li, JiaRui,Cai, Yu-Dong,et al. Computational Method for Distinguishing Lysine Acetylation, Sumoylation, and Ubiquitination using the Random Forest Algorithm with a Feature Selection Procedure[J]. COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING,2017,20(10):886-895.
APA Wang, ShaoPeng.,Li, JiaRui.,Cai, Yu-Dong.,Yuan, Fei.,Chen, Lei.,...&,.(2017).Computational Method for Distinguishing Lysine Acetylation, Sumoylation, and Ubiquitination using the Random Forest Algorithm with a Feature Selection Procedure.COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING,20(10),886-895.
MLA Wang, ShaoPeng,et al."Computational Method for Distinguishing Lysine Acetylation, Sumoylation, and Ubiquitination using the Random Forest Algorithm with a Feature Selection Procedure".COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING 20.10(2017):886-895.

入库方式： OAI收割

来源：上海营养与健康研究所

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