A comprehensive survey on computational methods of non-coding RNA and disease association prediction.

Journal: Briefings in bioinformatics
Published Date:

Abstract

The studies on relationships between non-coding RNAs and diseases are widely carried out in recent years. A large number of experimental methods and technologies of producing biological data have also been developed. However, due to their high labor cost and production time, nowadays, calculation-based methods, especially machine learning and deep learning methods, have received a lot of attention and been used commonly to solve these problems. From a computational point of view, this survey mainly introduces three common non-coding RNAs, i.e. miRNAs, lncRNAs and circRNAs, and the related computational methods for predicting their association with diseases. First, the mainstream databases of above three non-coding RNAs are introduced in detail. Then, we present several methods for RNA similarity and disease similarity calculations. Later, we investigate ncRNA-disease prediction methods in details and classify these methods into five types: network propagating, recommend system, matrix completion, machine learning and deep learning. Furthermore, we provide a summary of the applications of these five types of computational methods in predicting the associations between diseases and miRNAs, lncRNAs and circRNAs, respectively. Finally, the advantages and limitations of various methods are identified, and future researches and challenges are also discussed.

Authors

  • Xiujuan Lei
  • Thosini Bamunu Mudiyanselage
    Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA.
  • Yuchen Zhang
    School of Computer Science, Shaanxi Normal University, Xi'an, China.
  • Chen Bian
    School of Computer Science, Shaanxi Normal University, Xi'an, China.
  • Wei Lan
    School of Computer, Electronics and Information, Guangxi University, 100 Daxue East Road, Nanning, 530004, China.
  • Ning Yu
    Department of Computing Sciences, The College at Brockport, State University of New York, 350 New Campus Drive, Brockport, 14420, NY, USA. nyu@brockport.edu.
  • Yi Pan
    Department of Neurosis and Psychosomatic Diseases, Huzhou Third Municipal Hospital, The Affiliated Hospital of Huzhou University, Huzhou, Zhejiang, China.