LncDisAP: A computation model for LncRNA-disease association prediction based on multiple biological datasets

Background: Over the past decades, a large number of long non-coding RNAs (lncRNAs) have been identified. Growing evidence has indicated that the mutation and dysregulation of lncRNAs play a critical role in the development of many complex human diseases. Consequently, identifying potential disease-related lncRNAs is an effective means to improve the quality of disease diagnostics and treatment, which is the motivation of this work. Here, we propose a computational model (LncDisAP) for potential disease-related lncRNA identification based on multiple biological datasets. First, the associations between lncRNA and different data sources are collected from different databases. With these data sources as dimensions, we calculate the functional associations between lncRNAs by the recommendation strategy of collaborative filtering. Subsequently, a disease-associated lncRNA functional network is built with functional similarities between lncRNAs as the weight. Ultimately, potential disease-related lncRNAs can be identified based on ranked scores derived by random walking with restart (RWR). Then, training sets and testing sets are extracted from two different versions of a disease-lncRNA dataset to assess the performance of LncDisAP on 54 diseases. Results: A lncRNA functional network is built based on the proposed computational model, and it contains 66,060 associations among 364 lncRNAs associated with 182 diseases in total. We extract 218 known disease-lncRNA pairs associated with 54 diseases to assess the network. As a result, the average AUC (area under the receiver operating characteristic curve) of LncDisAP is 78.08%. Conclusion: In this article, a computational model integrating multiple lncRNA-related biological datasets is proposed for identifying potential disease-related lncRNAs. The result shows that LncDisAP is successful in predicting novel disease-related lncRNA signatures. In addition, with several common cancers taken as case studies, we found some unknown lncRNAs that could be associated with these diseases through our network. These results suggest that this method can be helpful in improving the quality for disease diagnostics and treatment.