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用于预测长链非编码RNA-蛋白质相互作用的二分网络投影推荐算法

The Bipartite Network Projection-Recommended Algorithm for Predicting Long Non-coding RNA-Protein Interactions.

作者信息

Zhao Qi, Yu Haifan, Ming Zhong, Hu Huan, Ren Guofei, Liu Hongsheng

机构信息

School of Mathematics, Liaoning University, Shenyang 110036, China.

National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University, Shenzhen 518060, China; College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China.

出版信息

Mol Ther Nucleic Acids. 2018 Dec 7;13:464-471. doi: 10.1016/j.omtn.2018.09.020. Epub 2018 Sep 29.

Abstract

With the development of science and biotechnology, many evidences show that ncRNAs play an important role in the development of important biological processes, especially in chromatin modification, cell differentiation and proliferation, RNA progressing, human diseases, etc. Moreover, lncRNAs account for the majority of ncRNAs, and the functions of lncRNAs are expressed by the related RNA-binding proteins. It is well known that the experimental verification of lncRNA-protein relationships is a waste of time and expensive. So many time-saving and inexpensive computational methods are proposed to uncover potential lncRNA-protein interactions. In this work, we propose a novel computational method to predict the potential lncRNA-protein interactions with the bipartite network projection recommended algorithm (LPI-BNPRA). Our approach is a semi-supervised method based on the lncRNA similarity matrix, protein similarity matrix, and lncRNA-protein interaction matrix. Compared with three previous methods under the leave-one-out cross-validation, our model has a more high-confidence result with the AUC value of 0.8754 and the AUPR value of 0.6283. We also do case studies by the Mus musculus dataset to further reflect the reliability of our approach. This suggests that LPI-BNPRA will be a reliable computational method to uncover lncRNA-protein interactions in biomedical research.

摘要

随着科学和生物技术的发展,许多证据表明非编码RNA在重要生物过程的发展中发挥着重要作用,特别是在染色质修饰、细胞分化与增殖、RNA进程、人类疾病等方面。此外,长链非编码RNA占非编码RNA的大部分,其功能由相关的RNA结合蛋白来表达。众所周知,对长链非编码RNA与蛋白质关系进行实验验证既浪费时间又成本高昂。因此,人们提出了许多省时且廉价的计算方法来揭示潜在的长链非编码RNA与蛋白质的相互作用。在这项工作中,我们提出了一种新的计算方法,即利用二分网络投影推荐算法(LPI-BNPRA)来预测潜在的长链非编码RNA与蛋白质的相互作用。我们的方法是一种基于长链非编码RNA相似性矩阵、蛋白质相似性矩阵和长链非编码RNA-蛋白质相互作用矩阵的半监督方法。在留一法交叉验证下与之前的三种方法相比,我们的模型具有更高置信度的结果,AUC值为0.8754,AUPR值为0.6283。我们还通过小家鼠数据集进行了案例研究,以进一步反映我们方法的可靠性。这表明LPI-BNPRA将是生物医学研究中揭示长链非编码RNA与蛋白质相互作用的一种可靠计算方法。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/80ca/6205413/f45fc2038e60/gr1.jpg

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