Unification of miRNA and isomiR research: The mirGFF3 format and the mirtop API

Thomas Desvignes, Phillipe Loher, Karen Eilbeck, Jeffery Ma, Gianvito Urgese, Bastian Fromm, Jason Sydes, Ernesto Aparicio-Puerta, Victor Barrera, Roderic Espín, Florian Thibord, Xavier Bofill De Ros, Eric Londin, Aristeidis G. Telonis, Elisa Ficarra, Marc R. Friedländer, John H. Postlethwait, Isidore Rigoutsos, Michael Hackenberg, Ioannis S. VlachosMarc K. Halushka, Lorena Pantano

Research output: Contribution to journalArticle

Abstract

Motivation: MicroRNAs (miRNAs) are small RNA molecules (~22 nucleotide long) involved in post-transcriptional gene regulation. Advances in high-throughput sequencing technologies led to the discovery of isomiRs, which are miRNA sequence variants. While many miRNA-seq analysis tools exist, the diversity of output formats hinders accurate comparisons between tools and precludes data sharing and the development of common downstream analysis methods. Results: To overcome this situation, we present here a community-based project, miRNA Transcriptomic Open Project (miRTOP) working towards the optimization of miRNA analyses. The aim of miRTOP is to promote the development of downstream isomiR analysis tools that are compatible with existing detection and quantification tools. Based on the existing GFF3 format, we first created a new standard format, mirGFF3, for the output of miRNA/ isomiR detection and quantification results from small RNA-seq data. Additionally, we developed a command line Python tool, mirtop, to create and manage the mirGFF3 format. Currently, mirtop can convert into mirGFF3 the outputs of commonly used pipelines, such as seqbuster, isomiR-SEA, sRNAbench, Prost! as well as BAM files. Some tools have also incorporated the mirGFF3 format directly into their code, such as, miRge2.0, IsoMIRmap and OptimiR. Its open architecture enables any tool or pipeline to output or convert results into mirGFF3. Collectively, this isomiR categorization system, along with the accompanying mirGFF3 and mirtop API, provide a comprehensive solution for the standardization of miRNA and isomiR annotation, enabling data sharing, reporting, comparative analyses and benchmarking, while promoting the development of common miRNA methods focusing on downstream steps of miRNA detection, annotation and quantification.

Original languageEnglish (US)
Pages (from-to)698-703
Number of pages6
JournalBioinformatics
Volume36
Issue number3
DOIs
StatePublished - Feb 2020

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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    Desvignes, T., Loher, P., Eilbeck, K., Ma, J., Urgese, G., Fromm, B., Sydes, J., Aparicio-Puerta, E., Barrera, V., Espín, R., Thibord, F., Ros, X. B. D., Londin, E., Telonis, A. G., Ficarra, E., Friedländer, M. R., Postlethwait, J. H., Rigoutsos, I., Hackenberg, M., ... Pantano, L. (2020). Unification of miRNA and isomiR research: The mirGFF3 format and the mirtop API. Bioinformatics, 36(3), 698-703. https://doi.org/10.1093/bioinformatics/btz675