[1]CHANG Zheng,MENG Jun,SHI Yunsheng,et al.LncRNA recognition by fusing multiple features and its function prediction[J].CAAI Transactions on Intelligent Systems,2018,13(6):928-934.[doi:10.11992/tis.201806008]
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LncRNA recognition by fusing multiple features and its function prediction

CAAI Transactions on Intelligent Systems[ISSN 1673-4785/CN 23-1538/TP] Volume: 13 Number of periods: 2018 6 Page number: 928-934 Column: 学术论文—机器学习 Public date: 2018-10-25
Title:
LncRNA recognition by fusing multiple features and its function prediction
Author(s):
CHANG Zheng;  MENG Jun;  SHI Yunsheng;  MO Fengran
School of Computer Science and Technology, Dalian University of Technology, Dalian 116023, China
Keywords:
lncRNA; identification; feature extraction; multiple features fusion; machine learning; interrelationship; network construction; function prediction
CLC:
TP391
DOI:
10.11992/tis.201806008
Abstract:
Considering the limitations of the traditional plant lncRNA identification based on a single feature, in this paper, a method, in which the open reading frame, secondary structure, and k-mers features of RNA sequences are integrated, is proposed. It involves the training of three classical classification models, Gaussian naive Bayes, support vector machines, and gradient lifting decision tree, and integrating the classification results. The performance of the method was evaluated using cross-validation, and it exhibited superior performance. The accuracy of the proposed method reached 89% when tested with the Arabidopsis thaliana dataset. Using the same dataset, the proposed method outperformed the popular CPAT, CNCI, and PLEK prediction software. In addition, based on the endogenous competition rules and RNA structure information, target prediction and filter rules for lncRNA-microRNA and microRNA-mRNA pairs were executed, and then related tools were used to establish RNA interaction regulatory networks, and the regulatory relationship was analyzed to predict the functions of lncRNAs in modules. Through Gene Ontology term analysis, the possible biological regulation function of lncRNAs can be predicted, and their corresponding functions can be inferred.
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