Combining Results from Distinct MicroRNA Target Prediction Tools Enhances the Performance of Analyses

Autor(es)

Oliveira, Arthur C. ; Bovolenta, Luiz A. ; Nachtigall, Pedro G. ; Herkenhoff, Marcos E. ; Lemke, Ney ; Pinhal, Danillo

• Tipo de documento: Artigo Científico
• Fonte: FRONTIERS IN GENETICS; v. 8, MAY 16 2017.
• Citações Web of Science: 11

Resumo

Target prediction is generally the first step toward recognition of bona fide microRNA (miRNA)-target interactions in living cells. Several target prediction tools are now available, which use distinct criteria and stringency to provide the best set of candidate targets for a single miRNA or a subset of miRNAs. However, there are many false-negative predictions, and consensus about the optimum strategy to select and use the output information provided by the target prediction tools is lacking. We compared the performance of four tools cited in literature-TargetScan (TS), miRanda-mirSVR (MR), Pita, and RNA22 (R22), and we determined the most effective approach for analyzing target prediction data (individual, union, or intersection). For this purpose, we calculated the sensitivity, specificity, precision, and correlation of these approaches using 10 miRNAs (miR-1-3p, miR-17-5p, miR-21-5p, miR-24-3p, miR-29a-3p, miR34a-5p, miR-124-3p, miR-125b-5p, miR-145-5p, and miR-155-5p) and 1,400 genes (700 validated and 700 non-validated) as targets of these miRNAs. The four tools provided a subset of high-quality predictions and returned few false-positive predictions; however, they could not identify several known true targets. We demonstrate that union of TS/MR and TS/MR/R22 enhanced the quality of in silico prediction analysis of miRNA targets. We conclude that the union rather than the intersection of the aforementioned tools is the best strategy for maximizing performance while minimizing the loss of time and resources in subsequent in vivo and in vitro experiments for functional validation of miRNA-target interactions. (AU)

• Processo FAPESP: 14/03062-0 - Caracterização molecular de híbridos heteróticos das linhagens Red Stirling e Chitralada da Tilápia do Nilo (Oreochromis niloticus)
• Beneficiário: Marcos Edgar Herkenhoff
• Modalidade de apoio: Bolsas no Brasil - Doutorado
• Processo FAPESP: 13/06864-7 - Análise funcional de microRNAs no desenvolvimento cardíaco de peixes por RNA-seq e genética reversa
• Beneficiário: Pedro Gabriel Nachtigall
• Modalidade de apoio: Bolsas no Brasil - Doutorado
• Processo FAPESP: 12/13450-1 - Análise exploratória em larga escala de miRNAs expressos em tilápia do Nilo utilizando ferramentas de bioinformática.
• Beneficiário: Luiz Augusto Bovolenta
• Modalidade de apoio: Bolsas no Brasil - Doutorado
• Processo FAPESP: 15/19176-7 - Investigando variações e funções de pequenos RNAs não-codificantes em Oreochromis niloticus
• Beneficiário: Luiz Augusto Bovolenta
• Modalidade de apoio: Bolsas no Exterior - Estágio de Pesquisa - Doutorado