MiRNA-BD: an evidence-based bioinformatics model and software tool for microRNA biomarker discovery

RNA Biol. 2018;15(8):1093-1105. doi: 10.1080/15476286.2018.1502590. Epub 2018 Sep 17.

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs with the potential as biomarkers for disease diagnosis, prognosis and therapy. In the era of big data and biomedical informatics, computer-aided biomarker discovery has become the current frontier. However, most of the computational models are highly dependent on specific prior knowledge and training-testing procedures, very few are mechanism-guided or evidence-based. To the best of our knowledge, untill now no general rules have been uncovered and applied to miRNA biomarker screening. In this study, we manually collected literature-reported cancer miRNA biomarkers and analyzed their regulatory patterns, including the regulatory modes, biological functions and evolutionary characteristics of their targets in the human miRNA-mRNA network. Two evidences were statistically detected and used to distinguish biomarker miRNAs from others. Based on these observations, we developed a novel bioinformatics model and software tool for miRNA biomarker discovery ( http://sysbio.suda.edu.cn/MiRNA-BD/ ). In contrast to routine methods that focus on miRNA synergic functions, our method searches for vulnerable sites in the miRNA-mRNA network and considers the independent regulatory power of miRNAs, i.e., single-line regulations between miRNAs and mRNAs. The performance comparison demonstrates the generality and precision of our model, which identifies miRNA biomarkers for cancers as well as other complex diseases without training or specific prior knowledge.

Keywords: Evidence-based bioinformatics model; miRNA biomarker discovery; miRNA-mRNA network analysis; single-line regulation mode.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biomarkers, Tumor / genetics*
  • Computational Biology / methods*
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic
  • Gene Regulatory Networks
  • Humans
  • MicroRNAs / genetics*
  • Neoplasms / diagnosis*
  • Neoplasms / genetics
  • RNA, Messenger / genetics*
  • Software*

Substances

  • Biomarkers, Tumor
  • MicroRNAs
  • RNA, Messenger

Grant support

This study was supported by the National Natural Science Foundation of China (Grant Nos. 31670851, 31470821, and 91530320) and National Key R&D programs of China (Grant No. 2016YFC1306605).