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Accurate Prediction of ncRNA-Protein Interactions From the Integration of Sequence and Evolutionary Information
Zhan, ZH (Zhan, Zhao-Hui)[ 1 ]; You, ZH (You, Zhu-Hong)[ 2 ]; Li, LP (Li, Li-Ping)[ 2 ]; Zhou, Y (Zhou, Yong)[ 1 ]; Yi, HC (Yi, Hai-Cheng)[ 2 ]
2018
发表期刊FRONTIERS IN GENETICS
ISSN1664-8021
卷号9期号:10页码:1-9
摘要

Non-coding RNA (ncRNA) plays a crucial role in numerous biological processes including gene expression and post-transcriptional gene regulation. The biological function of ncRNA is mostly realized by binding with related proteins. Therefore, an accurate understanding of interactions between ncRNA and protein has a significant impact on current biological research. The major challenge at this stage is the waste of a great deal of redundant time and resource consumed on classification in traditional interaction pattern prediction methods. Fortunately, an efficient classifier named LightGBM can solve this difficulty of long time consumption. In this study, we employed LightGBM as the integrated classifier and proposed a novel computational model for predicting ncRNA and protein interactions. More specifically, the pseudo-Zernike Moments and singular value decomposition algorithm are employed to extract the discriminative features from protein and ncRNA sequences. On four widely used datasets RP1369, RP1488, RPI1807, and RPI2241, we evaluated the performance of LGBM and obtained an superior performance with AUC of 0.799, 0.914, 0.989, and 0.762, respectively. The experimental results of 10-fold cross-validation shown that the proposed method performs much better than existing methods in predicting ncRNA-protein interaction patterns, which could be used as a useful tool in proteomics research.

关键词Ncrna-protein Interactions Pssm Lightgbm Pseudo-zernike Moments K-mers
DOI10.3389/fgene.2018.00458
收录类别SCI
WOS记录号WOS:000446620500001
引用统计
文献类型期刊论文
条目标识符http://ir.xjipc.cas.cn/handle/365002/5590
专题多语种信息技术研究室
通讯作者You, ZH (You, Zhu-Hong)[ 2 ]
作者单位1.China Univ Min & Technol, Sch Comp Sci & Technol, Xuzhou, Jiangsu, Peoples R China
2.Chinese Acad Sci, Xinjiang Tech Inst Phys & Chem, Urumqi, Peoples R China
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GB/T 7714
Zhan, ZH ,You, ZH ,Li, LP ,et al. Accurate Prediction of ncRNA-Protein Interactions From the Integration of Sequence and Evolutionary Information[J]. FRONTIERS IN GENETICS,2018,9(10):1-9.
APA Zhan, ZH ,You, ZH ,Li, LP ,Zhou, Y ,&Yi, HC .(2018).Accurate Prediction of ncRNA-Protein Interactions From the Integration of Sequence and Evolutionary Information.FRONTIERS IN GENETICS,9(10),1-9.
MLA Zhan, ZH ,et al."Accurate Prediction of ncRNA-Protein Interactions From the Integration of Sequence and Evolutionary Information".FRONTIERS IN GENETICS 9.10(2018):1-9.
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