Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation

doi:10.1186/1471-2105-12-409

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	Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation
	Ren, Xianwen 3,4; Wang, Yong-Cui 2,5; Wang, Yong1 ; Zhang, Xiang-Sun1 ; Deng, Nai-Yang 2
	2011-10-24
发表期刊	BMC BIOINFORMATICS
ISSN	1471-2105
卷号	12 页码:9
摘要	Background: With the development of genome-sequencing technologies, protein sequences are readily obtained by translating the measured mRNAs. Therefore predicting protein-protein interactions from the sequences is of great demand. The reason lies in the fact that identifying protein-protein interactions is becoming a bottleneck for eventually understanding the functions of proteins, especially for those organisms barely characterized. Although a few methods have been proposed, the converse problem, if the features used extract sufficient and unbiased information from protein sequences, is almost untouched. Results: In this study, we interrogate this problem theoretically by an optimization scheme. Motivated by the theoretical investigation, we find novel encoding methods for both protein sequences and protein pairs. Our new methods exploit sufficiently the information of protein sequences and reduce artificial bias and computational cost. Thus, it significantly outperforms the available methods regarding sensitivity, specificity, precision, and recall with cross-validation evaluation and reaches similar to 80% and similar to 90% accuracy in Escherichia coli and Saccharomyces cerevisiae respectively. Our findings here hold important implication for other sequence-based prediction tasks because representation of biological sequence is always the first step in computational biology. Conclusions: By considering the converse problem, we propose new representation methods for both protein sequences and protein pairs. The results show that our method significantly improves the accuracy of protein-protein interaction predictions.
DOI	10.1186/1471-2105-12-409
语种	英语
资助项目	Natural Science Foundation of China[60873205] ; Natural Science Foundation of China[10801131] ; Natural Science Foundation of China[10631070] ; Natural Science Foundation of China[10971223] ; Natural Science Foundation of China[11071252] ; Chinese Academy of Sciences[kjcx-yw-s7]
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS记录号	WOS:000296959500001
出版者	BIOMED CENTRAL 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/191
专题	应用数学研究所
通讯作者	Zhang, Xiang-Sun
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China 2.Chinese Agr Univ, Coll Sci, Beijing 100083, Peoples R China 3.Chinese Acad Med Sci, State Key Lab Mol Virol & Genet Engn, Inst Pathogen Biol, Beijing 100730, Peoples R China 4.Peking Union Med Coll, Beijing 100730, Peoples R China 5.Chinese Acad Sci, NW Inst Plateau Biol, Key Lab Adaptat & Evolut Plateau Biota, Xining 810001, Peoples R China
推荐引用方式 GB/T 7714	Ren, Xianwen,Wang, Yong-Cui,Wang, Yong,et al. Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation[J]. BMC BIOINFORMATICS,2011,12:9.
APA	Ren, Xianwen,Wang, Yong-Cui,Wang, Yong,Zhang, Xiang-Sun,&Deng, Nai-Yang.(2011).Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation.BMC BIOINFORMATICS,12,9.
MLA	Ren, Xianwen,et al."Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation".BMC BIOINFORMATICS 12(2011):9.