Sequence-based protein-protein interaction prediction via support vector machine

NWIPB OpenIR

	Sequence-based protein-protein interaction prediction via support vector machine
	Wang, Yongcui ; Wang, Jiguang ; Yang, Zhixia ; Deng, Naiyang
	2010-10-01
发表期刊	JOURNAL OF SYSTEMS SCIENCE & COMPLEXITY ; Wang, YC; Wang, JG; Yang, ZX; Deng, NY.Sequence-based protein-protein interaction prediction via support vector machine,JOURNAL OF SYSTEMS SCIENCE & COMPLEXITY,2010,23(5):1012-1023
摘要	This paper develops sequence-based methods for identifying novel protein-protein interactions (PPIs) by means of support vector machines (SVMs). The authors encode proteins ont only in the gene level but also in the amino acid level, and design a procedure to select negative training set for dealing with the training dataset imbalance problem, i.e., the number of interacting protein pairs is scarce relative to large scale non-interacting protein pairs. The proposed methods are validated on PPIs data of Plasmodium falciparum and Escherichia coli, and yields the predictive accuracy of 93.8% and 95.3%, respectively. The functional annotation analysis and database search indicate that our novel predictions are worthy of future experimental validation. The new methods will be useful supplementary tools for the future proteomics studies.; This paper develops sequence-based methods for identifying novel protein-protein interactions (PPIs) by means of support vector machines (SVMs). The authors encode proteins ont only in the gene level but also in the amino acid level, and design a procedure to select negative training set for dealing with the training dataset imbalance problem, i.e., the number of interacting protein pairs is scarce relative to large scale non-interacting protein pairs. The proposed methods are validated on PPIs data of Plasmodium falciparum and Escherichia coli, and yields the predictive accuracy of 93.8% and 95.3%, respectively. The functional annotation analysis and database search indicate that our novel predictions are worthy of future experimental validation. The new methods will be useful supplementary tools for the future proteomics studies.
文献类型	期刊论文
条目标识符	http://210.75.249.4/handle/363003/35789
专题	中国科学院西北高原生物研究所
推荐引用方式 GB/T 7714	Wang, Yongcui,Wang, Jiguang,Yang, Zhixia,et al. Sequence-based protein-protein interaction prediction via support vector machine[J]. JOURNAL OF SYSTEMS SCIENCE & COMPLEXITY, Wang, YC; Wang, JG; Yang, ZX; Deng, NY.Sequence-based protein-protein interaction prediction via support vector machine,JOURNAL OF SYSTEMS SCIENCE & COMPLEXITY,2010,23(5):1012-1023,2010.
APA	Wang, Yongcui,Wang, Jiguang,Yang, Zhixia,&Deng, Naiyang.(2010).Sequence-based protein-protein interaction prediction via support vector machine.JOURNAL OF SYSTEMS SCIENCE & COMPLEXITY.
MLA	Wang, Yongcui,et al."Sequence-based protein-protein interaction prediction via support vector machine".JOURNAL OF SYSTEMS SCIENCE & COMPLEXITY (2010).