Phogly-PseAAC: Prediction of lysine phosphoglycerylation in proteins incorporating with position-specific propensity

doi:10.1016/j.jtbi.2015.04.016

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	Phogly-PseAAC: Prediction of lysine phosphoglycerylation in proteins incorporating with position-specific propensity
	Xu, Yan 1; Ding, Ya-Xin 1; Ding, Jun 1; Wu, Ling-Yun2 ; Deng, Nai-Yang 3
	2015-08-21
发表期刊	JOURNAL OF THEORETICAL BIOLOGY
ISSN	0022-5193
卷号	379 页码:10-15
摘要	Large-scale characterization of post-translational modifications (PTMs), such as posphorylation, acetylation and ubiquitination, has highlighted their importance in the regulation of a myriad of signaling events. However, as another type of PTMs-lysine phosphoglycerylation, the data of phosphoglycerylated sites has just been manually experimented in recent years. Given an uncharacterized protein sequence that contains many lysine residues, which one of them can be phosphoglycerylated and which one not? This is a challenging problem. In view of this, establishing a useful computational method and developing an efficient predictor are highly desired. Here a new predictor named Phogly-PseAAC was developed which incorporated with the position specific amino acid propensity. The feature importance through F-score value has also been ranked. The predictor with the best feature set obtained the accuracy 75.10%, sensitivity 68.87%, specificity 75.57% and MCC 0.2538 in LOO test cross validation with center nearest neighbor algorithm. Meanwhile, a web-server for Phogly-PseAAC is accessible at http://app.aporc.org/Phogly-PseAAC/. For the convenience of most experimental scientists, we have further provided a brief instruction for the web-server, by which users can easily get their desired results without the need to follow the complicated mathematics presented in this paper. It is anticipated that Phogly-PseAAC may become a useful high throughput tool for identifying the lysine phosphoglycerylation sites. (C) 2015 Elsevier Ltd. All rights reserved.
关键词	Amino acid propensity F-score Phosphoglycerylation
DOI	10.1016/j.jtbi.2015.04.016
语种	英语
资助项目	National Natural Science Foundation of China[11301024] ; National Natural Science Foundation of China[11371365] ; National Natural Science Foundation of China[31201002] ; National Natural Science Foundation of China[11131009]
WOS研究方向	Life Sciences & Biomedicine - Other Topics ; Mathematical & Computational Biology
WOS类目	Biology ; Mathematical & Computational Biology
WOS记录号	WOS:000356839700002
出版者	ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/20159
专题	应用数学研究所
通讯作者	Xu, Yan
作者单位	1.Univ Sci & Technol Beijing, Dept Informat & Comp Sci, Beijing 100083, Peoples R China 2.Chinese Acad Sci, Inst Appl Math, Acad Math & Syst Sci, Beijing 100190, Peoples R China 3.China Agr Univ, Coll Sci, Beijing 100083, Peoples R China
推荐引用方式 GB/T 7714	Xu, Yan,Ding, Ya-Xin,Ding, Jun,et al. Phogly-PseAAC: Prediction of lysine phosphoglycerylation in proteins incorporating with position-specific propensity[J]. JOURNAL OF THEORETICAL BIOLOGY,2015,379:10-15.
APA	Xu, Yan,Ding, Ya-Xin,Ding, Jun,Wu, Ling-Yun,&Deng, Nai-Yang.(2015).Phogly-PseAAC: Prediction of lysine phosphoglycerylation in proteins incorporating with position-specific propensity.JOURNAL OF THEORETICAL BIOLOGY,379,10-15.
MLA	Xu, Yan,et al."Phogly-PseAAC: Prediction of lysine phosphoglycerylation in proteins incorporating with position-specific propensity".JOURNAL OF THEORETICAL BIOLOGY 379(2015):10-15.