Effectiveness and Usability of Bioinformatics Tools to Analyze Pathways Associated with miRNA Expression

MiRNAs are small, nonprotein-coding RNA molecules involved in gene regulation. While bioinformatics help guide miRNA research, it is less clear how they perform when studying biological pathways. We used 13 criteria to evaluate effectiveness and usability of existing bioinformatics tools. We evaluated the performance of six bioinformatics tools with a cluster of 12 differentially expressed miRNAs in colorectal tumors and three additional sets of 12 miRNAs that are not part of a known cluster. MiRPath performed the best of all the tools in linking miRNAs, with 92% of all miRNAs linked as well as the highest based on our established criteria followed by Ingenuity (58% linked). Other tools, including Empirical Gene Ontology, miRó, miRMaid, and PhenomiR, were limited by their lack of available tutorials, lack of flexibility and interpretability, and/or difficulty using the tool. In summary, we observed a lack of standardization across bioinformatic tools and a general lack of specificity in terms of pathways identified between groups of miRNAs. Hopefully, this evaluation will help guide the development of new tools.