title: A computational framework to infer human disease-associated long noncoding RNAs.
abstract: As a major class of noncoding RNAs, long noncoding RNAs (lncRNAs) have been implicated in various critical biological processes. Accumulating researches have linked dysregulations and mutations of lncRNAs to a variety of human disorders and diseases. However, to date, only a few human lncRNAs have been associated with diseases. Therefore, it is very important to develop a computational method to globally predict potential associated diseases for human lncRNAs. In this paper, we developed a computational framework to accomplish this by combining human lncRNA expression profiles, gene expression profiles, and human disease-associated gene data. Applying this framework to available human long intergenic noncoding RNAs (lincRNAs) expression data, we showed that the framework has reliable accuracy. As a result, for non-tissue-specific lincRNAs, the AUC of our algorithm is 0.7645, and the prediction accuracy is about 89%. This study will be helpful for identifying novel lncRNAs for human diseases, which will help in understanding the roles of lncRNAs in human diseases and facilitate treatment. The corresponding codes for our method and the predicted results are all available at http://asdcd.amss.ac.cn/MingXiLiu/lncRNA-disease.html.
authors.affiliation: Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China ; University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Ming-Xi
authors.initials: MX
authors.lastname: Liu
authors.affiliation: Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China ; National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing, China.
authors.forename: Xing
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing, China.
authors.forename: Geng
authors.initials: G
authors.lastname: Chen
authors.affiliation: Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing, China.
authors.forename: Qing-Hua
authors.initials: QH
authors.lastname: Cui
authors.affiliation: Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China ; National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing, China.
authors.forename: Gui-Ying
authors.initials: GY
authors.lastname: Yan
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D020022:Genetic Predisposition to Disease; D006801:Humans; D020407:Internet; D009928:Organ Specificity / Q000235:genetics; D062085:RNA, Long Noncoding; D012372:ROC Curve; D015203:Reproducibility of Results; D012984:Software
chemical_list: D062085:RNA, Long Noncoding