What's the target: understanding two decades of in silico microRNA-target prediction.

What's the target: understanding two decades of in silico microRNA-target prediction. Kern, F., Backes, C., Hirsch, P., Fehlmann, T., Hart, M., Meese, E., & Keller, A. Briefings in Bioinformatics, 2019.
doi abstract bibtex

Since the initial discovery of microRNAs as post-transcriptional, regulatory key players in the 1990s, a total number of \$2656\$ mature microRNAs have been publicly described for Homo sapiens. As discovery of new miRNAs is still on-going, target identification remains to be an essential and challenging step preceding functional annotation analysis. One key challenge for researchers seems to be the selection of the most appropriate tool out of the larger multiverse of published solutions for a given research study set-up.In this review we collectively describe the field of in silico target prediction in the course of time and point out long withstanding principles as well as recent developments. By compiling a catalog of characteristics about the 98 prediction methods and identifying common and exclusive traits, we signpost a simplified mechanism to address the problem of application selection. Going further we devised interpretation strategies for common types of output as generated by frequently used computational methods. To this end, our work specifically aims to make prospective users aware of common mistakes and practical questions that arise during the application of target prediction tools.An interactive implementation of our recommendations including materials shown in the manuscript is freely available at https://www.ccb.uni-saarland.de/mtguide.

@Article{10.1093/bib/bbz111,
  author       = {Fabian Kern and Christina Backes and Pascal Hirsch and Tobias Fehlmann and Martin Hart and Eckart Meese and Andreas Keller},
  title        = {What's the target: understanding two decades of in silico microRNA-target prediction.},
  journal      = {Briefings in Bioinformatics},
  year         = {2019},
  abstract     = {Since the initial discovery of microRNAs as post-transcriptional, regulatory key players in the 1990s, a total number of \\$2656\\$ mature microRNAs have been publicly described for Homo sapiens. As discovery of new miRNAs is still on-going, target identification remains to be an essential and challenging step preceding functional annotation analysis. One key challenge for researchers seems to be the selection of the most appropriate tool out of the larger multiverse of published solutions for a given research study set-up.In this review we collectively describe the field of in silico target prediction in the course of time and point out long withstanding principles as well as recent developments. By compiling a catalog of characteristics about the 98 prediction methods and identifying common and exclusive traits, we signpost a simplified mechanism to address the problem of application selection. Going further we devised interpretation strategies for common types of output as generated by frequently used computational methods. To this end, our work specifically aims to make prospective users aware of common mistakes and practical questions that arise during the application of target prediction tools.An interactive implementation of our recommendations including materials shown in the manuscript is freely available at https://www.ccb.uni-saarland.de/mtguide.},
  doi          = {10.1093/bib/bbz111},
  pii          = {10.1093/bib/bbz111},
}

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