Identifying novel associations between small molecules and miRNAs based on integrated molecular networks

Bioinformatics. 2015 Nov 15;31(22):3638-44. doi: 10.1093/bioinformatics/btv417. Epub 2015 Jul 20.


Motivation: miRNAs play crucial roles in human diseases and newly discovered could be targeted by small molecule (SM) drug compounds. Thus, the identification of small molecule drug compounds (SM) that target dysregulated miRNAs in cancers will provide new insight into cancer biology and accelerate drug discovery for cancer therapy.

Results: In this study, we aimed to develop a novel computational method to comprehensively identify associations between SMs and miRNAs. To this end, exploiting multiple molecular interaction databases, we first established an integrated SM-miRNA association network based on 690 561 SM to SM interactions, 291 600 miRNA to miRNA associations, as well as 664 known SM to miRNA targeting pairs. Then, by performing Random Walk with Restart algorithm on the integrated network, we prioritized the miRNAs associated to each of the SMs. By validating our results utilizing an independent dataset we obtained an area under the ROC curve greater than 0.7. Furthermore, comparisons indicated our integrated approach significantly improved the identification performance of those simple modeled methods. This computational framework as well as the prioritized SM-miRNA targeting relationships will promote the further developments of targeted cancer therapies.

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Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Area Under Curve
  • Computational Biology / methods
  • Gene Regulatory Networks*
  • Humans
  • MicroRNAs / genetics*
  • Reproducibility of Results
  • Small Molecule Libraries / metabolism*


  • MicroRNAs
  • Small Molecule Libraries