title: miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets.
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/.
authors.affiliation: YongLin Biomedical Engineering Center, National Taiwan University, Taipei, Taiwan.
authors.forename: Tzu-Pin
authors.initials: TP
authors.lastname: Lu
authors.forename: Chien-Yueh
authors.initials: CY
authors.lastname: Lee
authors.forename: Mong-Hsun
authors.initials: MH
authors.lastname: Tsai
authors.forename: Yu-Chiao
authors.initials: YC
authors.lastname: Chiu
authors.forename: Chuhsing Kate
authors.initials: CK
authors.lastname: Hsiao
authors.forename: Liang-Chuan
authors.initials: LC
authors.lastname: Lai
authors.forename: Eric Y
authors.initials: EY
authors.lastname: Chuang
mesh_terms: D000465:Algorithms; D000818:Animals; D030561:Databases, Nucleic Acid; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D035683:MicroRNAs