Advancing the prediction accuracy of protein-protein interactions by utilizing evolutionary information from position-specific scoring matrix and ensemble classifier
文献类型：期刊论文
| 作者 | Wang, L (Wang, Lei); You, ZH (You, Zhu-Hong) ; Xia, SX (Xia, Shi-Xiong); Liu, F (Liu, Feng); Chen, X (Chen, Xing); Yan, X (Yan, Xin); Zhou, Y (Zhou, Yong)
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| 刊名 | JOURNAL OF THEORETICAL BIOLOGY
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| 出版日期 | 2017 |
| 卷号 | 418期号:4页码:105-110 |
| 关键词 | Position-specific scoring matrix Multiple sequences alignments Rotation forest Cancer |
| 英文摘要 | Protein-Protein Interactions (PPIs) are essential to most biological processes and play a critical role in most cellular functions. With the development of high-throughput biological techniques and in si/ico methods, a large number of PPI data have been generated for various organisms, but many problems remain unsolved. These factors promoted the development of the in silico methods based on machine learning to predict PPIs. In this study, we propose a novel method by combining ensemble Rotation Forest (RF) classifier and Discrete Cosine Transform (DCT) algorithm to predict the interactions among proteins. Specifically, the protein amino acids sequence is transformed into Position-Specific Scoring Matrix (PSSM) containing biological evolution information, and then the feature vector is extracted to present protein evolutionary information using DCT algorithm; finally, the ensemble rotation forest model is used to predict whether a given protein pair is interacting or not. When performed on Yeast and H. pylori data sets, the proposed method achieved excellent results with an average accuracy of 98.54% and 88.27%. In addition, we achieved good prediction accuracy of 98.08%, 92.75%, 98.87% and 98.72% on independent data sets (C.elegans, E.coli, Hsapiens and M.muscu/us). In order to further evaluate the performance of our method, we compare it with the state-of-the-art Support Vector Machine (SVM) classifier and get good results. |
| 收录类别 | SCI |
| WOS记录号 | WOS:000397701300011 |
| 源URL | [http://ir.xjipc.cas.cn/handle/365002/4767]  |
| 专题 | 新疆理化技术研究所_多语种信息技术研究室 |
| 作者单位 | 1.China Univ Min & Technol, Sch Comp Sci & Technol, Xuzhou 221116, Jiangsu, Peoples R China 2.Zaozhuang Univ, Coll Informat Sci & Engn, Zaozhuang 277100, Shandong, Peoples R China 3.Chinese Acad Sci, Xinjiang Tech Inst Phys & Chem, Urumqi 830011, Peoples R China 4.China Natl Coal Assoc, Beijing 100713, Peoples R China 5.China Univ Min & Technol, Sch Informat & Control Engn, Xuzhou 221116, Jiangsu, Peoples R China 6.Zaozhuang Univ, Sch Foreign Languages, Zaozhuang 277100, Shandong, Peoples R China |
| 推荐引用方式 GB/T 7714 | Wang, L ,You, ZH ,Xia, SX ,et al. Advancing the prediction accuracy of protein-protein interactions by utilizing evolutionary information from position-specific scoring matrix and ensemble classifier[J]. JOURNAL OF THEORETICAL BIOLOGY,2017,418(4):105-110. |
| APA | Wang, L .,You, ZH .,Xia, SX .,Liu, F .,Chen, X .,...&Zhou, Y .(2017).Advancing the prediction accuracy of protein-protein interactions by utilizing evolutionary information from position-specific scoring matrix and ensemble classifier.JOURNAL OF THEORETICAL BIOLOGY,418(4),105-110. |
| MLA | Wang, L ,et al."Advancing the prediction accuracy of protein-protein interactions by utilizing evolutionary information from position-specific scoring matrix and ensemble classifier".JOURNAL OF THEORETICAL BIOLOGY 418.4(2017):105-110. |
入库方式： OAI收割
来源：新疆理化技术研究所
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