miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets

PLoS One. 2012;7(8):e42390. doi: 10.1371/journal.pone.0042390. Epub 2012 Aug 1.

Abstract

Background: Many prediction tools for microRNA (miRNA) targets have been developed, but inconsistent predictions were observed across multiple algorithms, which can make further analysis difficult. Moreover, the nomenclature of human miRNAs changes rapidly. To address these issues, we developed a web-based system, miRSystem, for converting queried miRNAs to the latest annotation and predicting the function of miRNA by integrating miRNA target gene prediction and function/pathway analyses.

Results: First, queried miRNA IDs were converted to the latest annotated version to prevent potential conflicts resulting from multiple aliases. Next, by combining seven algorithms and two validated databases, potential gene targets of miRNAs and their functions were predicted based on the consistency across independent algorithms and observed/expected ratios. Lastly, five pathway databases were included to characterize the enriched pathways of target genes through bootstrap approaches. Based on the enriched pathways of target genes, the functions of queried miRNAs could be predicted.

Conclusions: MiRSystem is a user-friendly tool for predicting the target genes and their associated pathways for many miRNAs simultaneously. The web server and the documentation are freely available at http://mirsystem.cgm.ntu.edu.tw/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Animals
  • Databases, Nucleic Acid*
  • Humans
  • Mice
  • MicroRNAs* / genetics
  • MicroRNAs* / metabolism
  • Sequence Analysis, RNA*
  • Software*

Substances

  • MicroRNAs

Grant support

This research was supported in part by NSC100-2314-B-002-054- from National Science Council, Taiwan and 99R81811 by National Taiwan University, Taiwan. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.