TZU-PIN LULee, C.-Y.C.-Y.LeeTsai, M.-H.M.-H.TsaiChiu, Y.-C.Y.-C.ChiuCHUHSING KATE HSIAOLIANG-CHUAN LAIERIC YAO-YU CHUANG2022-04-202022-04-20201219326203https://www.scopus.com/inward/record.uri?eid=2-s2.0-84864777932&doi=10.1371%2fjournal.pone.0042390&partnerID=40&md5=5ecd65d511afdf04b58df72bfb0d1265https://scholars.lib.ntu.edu.tw/handle/123456789/604938Background: 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/. © 2012 Lu et al.microRNA; algorithm; AREG gene; article; bootstrapping; CCDC135 gene; computer system; data base; FETUB gene; gene; gene function; gene targeting; GPHB5 gene; human; information processing; mouse; NME1 gene; nonhuman; nucleotide sequence; PPP1R14D gene; PSME1 gene; RNA analysis; RNA sequence; RTN4RL1 gene; SIPA1 gene; VRK2 gene; web browser; Algorithms; Animals; Databases, Nucleic Acid; Humans; Mice; MicroRNAs; Sequence Analysis, RNA; Softwarejournal article10.1371/journal.pone.0042390228703252-s2.0-84864777932