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NCPHLDA: a novel method for human lncRNA-disease association prediction based on network consistency projection

文献类型：期刊论文

作者Xie, Guobo1; Huang, Zecheng1; Liu, Zhenguo2; Lin, Zhiyi1; Ma, Lei3
刊名MOLECULAR OMICS
出版日期2019-12-01
卷号15期号:6页码:442-450
DOI10.1039/c9mo00092e
通讯作者Lin, Zhiyi(lzy291@gdut.edu.cn)
英文摘要In recent years, an increasing number of biological experiments and clinical reports have shown that lncRNA is closely related to the development of various complex human diseases. Therefore, studying the relationship between lncRNA and disease is necessary. Doing so not only helps to understand the disease mechanism, but also facilitates the diagnosis, treatment, and prognosis of disease. However, understanding the relationship between lncRNA and disease through biological experiments and clinical studies requires considerable time and money. Over the years, many researchers have developed computational methods to predict potential lncRNA-disease associations. In this study, on the basis of the assumption that functionally similar lncRNAs tend to associate with phenotypically similar diseases, and vice versa, we propose a novel computational method called network consistency projection for human lncRNA-disease associations (NCPHLDA) to predict potential lncRNA-disease associations. This method integrates a lncRNA cosine similarity network, a disease cosine similarity network, and the known lncRNA-disease association network. NCPHLDA is not only a parameterless method but also does not require a negative sample. More importantly, NCPHLDA can predict lncRNA without any known associated diseases. AUC values of 0.9273 and 0.9179 +/- 0.0043 are obtained by implementing leave-one-out cross-validation and 5-fold cross-validation for NCPHLDA, respectively. Case studies of three diseases (breast cancer, cervical cancer, and hepatocellular carcinoma) indicate that NCPHLDA has reliable predictive performance. The source code of NCPHLDA is freely available at ; https://github.com/bryanze/NCPHLDA.
WOS关键词LONG NONCODING RNAS ; BREAST-CANCER ; HEPATOCELLULAR-CARCINOMA ; FUNCTIONAL SIMILARITY ; CERVICAL-CANCER ; DOWN-REGULATION ; EXPRESSION ; GENOME ; IDENTIFICATION ; DATABASE
资助项目National Natural Science Foundation of China[618002072] ; National Natural Science Foundation of China[61702112] ; Natural Science Foundation of Guangdong Province[2018A030313389] ; Science and Technology Plan Project of Guangdong Province[2018B030323026] ; Science and Technology Plan Project of Guangdong Province[2017A040405050] ; Science and Technology Plan Project of Guangdong Province[2016B030306004] ; Science and Technology Plan Project of Guangdong Province[2015B010129014] ; Science and Technology Plan Project of Guangdong Province[2016B030301008]
WOS研究方向Biochemistry & Molecular Biology
语种英语
出版者ROYAL SOC CHEMISTRY
WOS记录号WOS:000501170000006
资助机构National Natural Science Foundation of China ; Natural Science Foundation of Guangdong Province ; Science and Technology Plan Project of Guangdong Province
源URL[http://ir.ia.ac.cn/handle/173211/29411]  
专题类脑芯片与系统研究
通讯作者Lin, Zhiyi
作者单位1.Guangdong Univ Technol, Sch Comp Sci, Guangzhou, Guangdong, Peoples R China
2.Sun Yat Sen Univ, Dept Thorac Surg, Affiliated Hosp 1, Guangzhou, Guangdong, Peoples R China
3.Chinese Acad Sci, Inst Automat, Beijing, Peoples R China
推荐引用方式
GB/T 7714		 Xie, Guobo,Huang, Zecheng,Liu, Zhenguo,et al. NCPHLDA: a novel method for human lncRNA-disease association prediction based on network consistency projection[J]. MOLECULAR OMICS,2019,15(6):442-450.
APA Xie, Guobo,Huang, Zecheng,Liu, Zhenguo,Lin, Zhiyi,&Ma, Lei.(2019).NCPHLDA: a novel method for human lncRNA-disease association prediction based on network consistency projection.MOLECULAR OMICS,15(6),442-450.
MLA Xie, Guobo,et al."NCPHLDA: a novel method for human lncRNA-disease association prediction based on network consistency projection".MOLECULAR OMICS 15.6(2019):442-450.

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来源：自动化研究所

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