title: Improved method for prioritization of disease associated lncRNAs based on ceRNA theory and functional genomics data.
abstract: Although several computational models that predict disease-associated lncRNAs (long non-coding RNAs) exist, only a limited number of disease-associated lncRNAs are known. In this study, we mapped lncRNAs to their functional genomics context using competing endogenous RNAs (ceRNAs) theory. Based on the criteria that similar lncRNAs are likely involved in similar diseases, we proposed a disease lncRNA prioritization method, DisLncPri, to identify novel disease-lncRNA associations. Using a leave-one-out cross validation (LOOCV) strategy, DisLncPri achieved reliable area under curve (AUC) values of 0.89 and 0.87 for the LncRNADisease and Lnc2Cancer datasets that further improved to 0.90 and 0.89 by integrating a multiple rank fusion strategy. We found that DisLncPri had the highest rank enrichment score and AUC value in comparison to several other methods for case studies of alzheimer's disease, ovarian cancer, pancreatic cancer and gastric cancer. Several novel lncRNAs in the top ranks of these diseases were found to be newly verified by relevant databases or reported in recent studies. Prioritization of lncRNAs from a microarray (GSE53622) of oesophageal cancer patients highlighted ENSG00000226029 (top 2), a previously unidentified lncRNA as a potential prognostic biomarker. Our analysis thus indicates that DisLncPri is an excellent tool for identifying lncRNAs that could be novel biomarkers and therapeutic targets in a variety of human diseases.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Wang
authors.affiliation: The First Affiliated Hospital, Harbin Medical University, Harbin, China.
authors.forename: Qiuyan
authors.initials: Q
authors.lastname: Guo
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Gao
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhi
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Liu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Jizhou
authors.initials: J
authors.lastname: Zhang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Yue
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Maoni
authors.initials: M
authors.lastname: Guo
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.|Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, China.
authors.forename: Shangwei
authors.initials: S
authors.lastname: Ning
authors.affiliation: The First Affiliated Hospital, Harbin Medical University, Harbin, China.
authors.forename: Guangmei
authors.initials: G
authors.lastname: Zhang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.|Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, China.
authors.forename: Xia
authors.initials: X
authors.lastname: Li
mesh_terms: D000544:Alzheimer Disease / Q000235:genetics; D019540:Area Under Curve; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D004938:Esophageal Neoplasms / Q000235:genetics; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D056726:Genetic Association Studies / Q000379:methods*; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D023281:Genomics; D006801:Humans; D008297:Male; D010051:Ovarian Neoplasms / Q000235:genetics; D010190:Pancreatic Neoplasms / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics*; D013274:Stomach Neoplasms / Q000235:genetics
chemical_list: D062085:RNA, Long Noncoding
keywords: competing endogenous RNA; functional genomics; long non-coding RNA; prognostic biomarker