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A Computational Framework to Infer Human Disease-Associated Long Noncoding RNAs

By Ming-Xi Liu, Xing Chen, Geng Chen, Qing-Hua Cui and Gui-Ying Yan

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.http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000329460100056&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701Multidisciplinary SciencesSCI(E)PubMed16ARTICLEcuiqinghua@hsc.pku.edu.cn; yangy@amss.ac.cn1e84408

Topics: GENE-EXPRESSION, BREAST-CANCER, DATABASE, GENOME, PROTEIN, INHIBITOR, MOUSE, OVEREXPRESSION, SUSCEPTIBILITY, IDENTIFICATION
Publisher: plos one
Year: 2014
DOI identifier: 10.1371/journal.pone.0084408
OAI identifier: oai:localhost:20.500.11897/190011
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