TY - JOUR
T1 - Unification of miRNA and isomiR research
T2 - The mirGFF3 format and the mirtop API
AU - Desvignes, Thomas
AU - Loher, Phillipe
AU - Eilbeck, Karen
AU - Ma, Jeffery
AU - Urgese, Gianvito
AU - Fromm, Bastian
AU - Sydes, Jason
AU - Aparicio-Puerta, Ernesto
AU - Barrera, Victor
AU - Espín, Roderic
AU - Thibord, Florian
AU - Ros, Xavier Bofill De
AU - Londin, Eric
AU - Telonis, Aristeidis G.
AU - Ficarra, Elisa
AU - Friedländer, Marc R.
AU - Postlethwait, John H.
AU - Rigoutsos, Isidore
AU - Hackenberg, Michael
AU - Vlachos, Ioannis S.
AU - Halushka, Marc K.
AU - Pantano, Lorena
N1 - Funding Information:
This work was supported by grant PLR-1543383 and OPP-1543383 of the National Science Foundation (T.D. and J.H.P.), B.F. and M.R.F. acknowledge funding from the Strategic Research Area (SFO) program of the Swedish Research Council (VR) through Stockholm University, M.K.H. was supported by grant 1R01HL137811 of the National Institutes of Health, National Heart Lung Blood Institute, F.T. was financially supported by the GENMED laboratory of excellence on medical genomics (ANR-10-LABX-0013) and I.S.V. was supported by the George and Marie Vergottis Fellowship of Harvard Medical School.
Publisher Copyright:
© The Author(s) 2019. Published by Oxford University Press. All rights reserved
PY - 2020/2
Y1 - 2020/2
N2 - 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.
AB - 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.
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U2 - 10.1093/bioinformatics/btz675
DO - 10.1093/bioinformatics/btz675
M3 - Article
C2 - 31504201
AN - SCOPUS:85079079762
VL - 36
SP - 698
EP - 703
JO - Bioinformatics
JF - Bioinformatics
SN - 1367-4803
IS - 3
ER -