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Lysine Malonylation Identification in E-coli with Multiple Features

文献类型：期刊论文

作者Shao, Yuanhai1; Wang, Hui2; Yang, Yingxi4; Xu, Yan3,4
刊名CURRENT PROTEOMICS
出版日期2019
卷号16期号:3页码:166-174
关键词Malonylation support vector machine post translational modification E. coli Receive Operating Character (ROC) Prokaryotes
ISSN号1570-1646
DOI10.2174/1570164615666181005104614
英文摘要Motivation: Lysine malonylation in eukaryote proteins had been found in 2011 through high-throughput proteomic analysis. However, it was poorly understood in prokaryotes. Recent researches have shown that maonylation in E. colt was significantly enriched in protein translation, energy metabolism pathways and fatty acid biosynthesis. Results: In this work we proposed a predictor to identify the lysine malonylation sites in E. coli through physicochemical properties, binary code and sequence frequency by support vector machine algorithm. The experimentally determined lysine malonylation sites were retrieved from the first and largest malonylome dataset in prokaryotes up to date. The physicochemical properties plus position specific amino acid sequence propensity features got the best results with AUC (the area under the Receive Operating Character curve) 0.7994, MCC (Mathew correlation coefficient) 0.4335 in 10-fold cross-validation. Meanwhile the AUC values were 0.7800, 0.7851 and 0.8050 in 6-fold, 8-fold and LOO (leave-one-out) cross-validation, respectively. All the ROC curves were close to each other which illustrated the robustness and performance of the proposed predictor. We also analyzed the sequence propensities through TwoSampleLogo and found some peptides differences with t-test p<0.01. The predictor had shown better results than those of other methods K-Nearest Neighbors, C4.5 decision tree, Naive Bayes and Random Forest. Functional analysis showed that malonylated proteins were involved in many transcription activities and diverse biological processes. Meanwhile we also developed an online package which could be freely downloaded https://github.com/Sunmile/Malonylation E.coli.
资助项目Natural Science Foundation of China[11671032] ; Fundamental Research Funds for the Central Universities[FRF-TP-17-024A2] ; Natural Science Foundation of Hainan Province[118QN181] ; Scientific Research Foundation of Hainan University[(sk)1804]
WOS研究方向Biochemistry & Molecular Biology
语种英语
WOS记录号WOS:000458617700001
出版者BENTHAM SCIENCE PUBL LTD
源URL[http://119.78.100.204/handle/2XEOYT63/3402]  
专题中国科学院计算技术研究所期刊论文_英文
通讯作者Shao, Yuanhai
作者单位1.Hainan Univ, Sch Econ & Management, Haikou 570228, Hainan, Peoples R China
2.Chinese Acad Sci, Inst Comp Technol, Beijing 100080, Peoples R China
3.Univ Sci & Technol Beijing, Beijing Key Lab Magnetophotoelect Composites & In, Beijing 100083, Peoples R China
4.Univ Sci & Technol Beijing, Dept Informat & Comp Sci, Beijing 100083, Peoples R China
推荐引用方式
GB/T 7714		 Shao, Yuanhai,Wang, Hui,Yang, Yingxi,et al. Lysine Malonylation Identification in E-coli with Multiple Features[J]. CURRENT PROTEOMICS,2019,16(3):166-174.
APA Shao, Yuanhai,Wang, Hui,Yang, Yingxi,&Xu, Yan.(2019).Lysine Malonylation Identification in E-coli with Multiple Features.CURRENT PROTEOMICS,16(3),166-174.
MLA Shao, Yuanhai,et al."Lysine Malonylation Identification in E-coli with Multiple Features".CURRENT PROTEOMICS 16.3(2019):166-174.

入库方式： OAI收割

来源：计算技术研究所

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