title: A Bipartite Network-based Method for Prediction of Long Non-coding RNA-protein Interactions.
abstract: As one large class of non-coding RNAs (ncRNAs), long ncRNAs (lncRNAs) have gained considerable attention in recent years. Mutations and dysfunction of lncRNAs have been implicated in human disorders. Many lncRNAs exert their effects through interactions with the corresponding RNA-binding proteins. Several computational approaches have been developed, but only few are able to perform the prediction of these interactions from a network-based point of view. Here, we introduce a computational method named lncRNA-protein bipartite network inference (LPBNI). LPBNI aims to identify potential lncRNA-interacting proteins, by making full use of the known lncRNA-protein interactions. Leave-one-out cross validation (LOOCV) test shows that LPBNI significantly outperforms other network-based methods, including random walk (RWR) and protein-based collaborative filtering (ProCF). Furthermore, a case study was performed to demonstrate the performance of LPBNI using real data in predicting potential lncRNA-interacting proteins.
authors.affiliation: School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China.
authors.forename: Mengqu
authors.initials: M
authors.lastname: Ge
authors.affiliation: School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China; Centers for Biomedical Engineering, University of Science and Technology of China, Hefei 230027, China. Electronic address: aoli@ustc.edu.cn.
authors.forename: Ao
authors.initials: A
authors.lastname: Li
authors.affiliation: School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China; Centers for Biomedical Engineering, University of Science and Technology of China, Hefei 230027, China.
authors.forename: Minghui
authors.initials: M
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D019540:Area Under Curve; D006801:Humans; D011485:Protein Binding; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D012372:ROC Curve; D060388:Support Vector Machine
chemical_list: D062085:RNA, Long Noncoding; D016601:RNA-Binding Proteins
keywords: Bipartite network; Interaction; Propagation; Protein; lncRNA