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; Eric Londin; Aristeidis G. Telonis; Elisa Ficarra; Marc R. Friedländer; John H. Postlethwait; Isidore Rigoutsos; Michael Hackenberg; Ioannis S. Vlachos; Marc K. Halushka; Lorena Pantano

doi:10.1101/505222

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, Eric Londin, Aristeidis G. Telonis, Elisa Ficarra, Marc R. Friedländer, John H. Postlethwait, Isidore Rigoutsos, Michael Hackenberg, Ioannis S. Vlachos, Marc K. Halushka, Lorena Pantano

School of Medicine

Research output: Contribution to journal › Article › peer-review

Abstract

Background 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, a lack of consensus on miRNA/isomiR analyses exists, and the resulting diversity of output formats hinders accurate comparisons between tools and precludes data sharing and the development of common downstream analysis methods. Findings To overcome this situation, we present here a community-based project, miRTOP (miRNA Transcriptomic Open Project) working towards the optimization of miRNA analyses. The aim of miRTOP is to promote the development of downstream analysis tools that are compatible with any existing detection and quantification tool. 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 manage the mirGFF3 format. Currently, mirtop can convert into mirGFF3 the outputs of commonly used pipelines, such as seqbuster, miRge2.0, isomiR-SEA, sRNAbench, and Prost!, as well as BAM files. Its open architecture enables any tool or pipeline to output results in mirGFF3. Conclusions Collectively a comprehensive isomiR categorization system, along with the accompanying mirGFF3 and mirtop API provide a complete solution for the standardization of miRNA and isomiR analysis, enabling data sharing, reporting, comparative analyses, and benchmarking, while promoting the development of common miRNA methods focusing on downstream steps to miRNA detection, annotation, and quantification.

Original language	English (US)
Journal	Unknown Journal
DOIs	https://doi.org/10.1101/505222
State	Published - Dec 25 2018

Keywords

file format
isomiR
microRNA
reproducibility
small RNA-seq
standardization

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology(all)
Agricultural and Biological Sciences(all)
Immunology and Microbiology(all)
Neuroscience(all)
Pharmacology, Toxicology and Pharmaceutics(all)

Access to Document

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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., Londin, E., Telonis, A. G., Ficarra, E., Friedländer, M. R., Postlethwait, J. H., Rigoutsos, I., Hackenberg, M., Vlachos, I. S., Halushka, M. K., & Pantano, L. (2018). Unification of miRNA and isomiR research: The mirGFF3 format and the mirtop API. Unknown Journal. https://doi.org/10.1101/505222

Unification of miRNA and isomiR research : The mirGFF3 format and the mirtop API. / Desvignes, Thomas; Loher, Phillipe; Eilbeck, Karen; Ma, Jeffery; Urgese, Gianvito; Fromm, Bastian; Sydes, Jason; Aparicio-Puerta, Ernesto; Barrera, Victor; Espín, Roderic; Londin, Eric; Telonis, Aristeidis G.; Ficarra, Elisa; Friedländer, Marc R.; Postlethwait, John H.; Rigoutsos, Isidore; Hackenberg, Michael; Vlachos, Ioannis S.; Halushka, Marc K.; Pantano, Lorena.

In: Unknown Journal, 25.12.2018.

Research output: Contribution to journal › Article › peer-review

Desvignes, T, Loher, P, Eilbeck, K, Ma, J, Urgese, G, Fromm, B, Sydes, J, Aparicio-Puerta, E, Barrera, V, Espín, R, Londin, E, Telonis, AG, Ficarra, E, Friedländer, MR, Postlethwait, JH, Rigoutsos, I, Hackenberg, M, Vlachos, IS, Halushka, MK & Pantano, L 2018, 'Unification of miRNA and isomiR research: The mirGFF3 format and the mirtop API', Unknown Journal. https://doi.org/10.1101/505222

Desvignes, Thomas ; Loher, Phillipe ; Eilbeck, Karen ; Ma, Jeffery ; Urgese, Gianvito ; Fromm, Bastian ; Sydes, Jason ; Aparicio-Puerta, Ernesto ; Barrera, Victor ; Espín, Roderic ; Londin, Eric ; Telonis, Aristeidis G. ; Ficarra, Elisa ; Friedländer, Marc R. ; Postlethwait, John H. ; Rigoutsos, Isidore ; Hackenberg, Michael ; Vlachos, Ioannis S. ; Halushka, Marc K. ; Pantano, Lorena. / Unification of miRNA and isomiR research : The mirGFF3 format and the mirtop API. In: Unknown Journal. 2018.

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title = "Unification of miRNA and isomiR research: The mirGFF3 format and the mirtop API",

abstract = " Background 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, a lack of consensus on miRNA/isomiR analyses exists, and the resulting diversity of output formats hinders accurate comparisons between tools and precludes data sharing and the development of common downstream analysis methods. Findings To overcome this situation, we present here a community-based project, miRTOP (miRNA Transcriptomic Open Project) working towards the optimization of miRNA analyses. The aim of miRTOP is to promote the development of downstream analysis tools that are compatible with any existing detection and quantification tool. 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, {\textquoteleft}mirtop{\textquoteright}, to manage the mirGFF3 format. Currently, mirtop can convert into mirGFF3 the outputs of commonly used pipelines, such as seqbuster, miRge2.0, isomiR-SEA, sRNAbench, and Prost!, as well as BAM files. Its open architecture enables any tool or pipeline to output results in mirGFF3. Conclusions Collectively a comprehensive isomiR categorization system, along with the accompanying mirGFF3 and mirtop API provide a complete solution for the standardization of miRNA and isomiR analysis, enabling data sharing, reporting, comparative analyses, and benchmarking, while promoting the development of common miRNA methods focusing on downstream steps to miRNA detection, annotation, and quantification.",

keywords = "file format, isomiR, microRNA, reproducibility, small RNA-seq, standardization",

author = "Thomas Desvignes and Phillipe Loher and Karen Eilbeck and Jeffery Ma and Gianvito Urgese and Bastian Fromm and Jason Sydes and Ernesto Aparicio-Puerta and Victor Barrera and Roderic Esp{\'i}n and Eric Londin and Telonis, {Aristeidis G.} and Elisa Ficarra and Friedl{\"a}nder, {Marc R.} and Postlethwait, {John H.} and Isidore Rigoutsos and Michael Hackenberg and Vlachos, {Ioannis S.} and Halushka, {Marc K.} and Lorena Pantano",

note = "Publisher Copyright: The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.",

year = "2018",

month = dec,

day = "25",

doi = "10.1101/505222",

language = "English (US)",

journal = "Advances in Water Resources",

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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 - 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 - Publisher Copyright: The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

PY - 2018/12/25

Y1 - 2018/12/25

N2 - Background 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, a lack of consensus on miRNA/isomiR analyses exists, and the resulting diversity of output formats hinders accurate comparisons between tools and precludes data sharing and the development of common downstream analysis methods. Findings To overcome this situation, we present here a community-based project, miRTOP (miRNA Transcriptomic Open Project) working towards the optimization of miRNA analyses. The aim of miRTOP is to promote the development of downstream analysis tools that are compatible with any existing detection and quantification tool. 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 manage the mirGFF3 format. Currently, mirtop can convert into mirGFF3 the outputs of commonly used pipelines, such as seqbuster, miRge2.0, isomiR-SEA, sRNAbench, and Prost!, as well as BAM files. Its open architecture enables any tool or pipeline to output results in mirGFF3. Conclusions Collectively a comprehensive isomiR categorization system, along with the accompanying mirGFF3 and mirtop API provide a complete solution for the standardization of miRNA and isomiR analysis, enabling data sharing, reporting, comparative analyses, and benchmarking, while promoting the development of common miRNA methods focusing on downstream steps to miRNA detection, annotation, and quantification.

AB - Background 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, a lack of consensus on miRNA/isomiR analyses exists, and the resulting diversity of output formats hinders accurate comparisons between tools and precludes data sharing and the development of common downstream analysis methods. Findings To overcome this situation, we present here a community-based project, miRTOP (miRNA Transcriptomic Open Project) working towards the optimization of miRNA analyses. The aim of miRTOP is to promote the development of downstream analysis tools that are compatible with any existing detection and quantification tool. 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 manage the mirGFF3 format. Currently, mirtop can convert into mirGFF3 the outputs of commonly used pipelines, such as seqbuster, miRge2.0, isomiR-SEA, sRNAbench, and Prost!, as well as BAM files. Its open architecture enables any tool or pipeline to output results in mirGFF3. Conclusions Collectively a comprehensive isomiR categorization system, along with the accompanying mirGFF3 and mirtop API provide a complete solution for the standardization of miRNA and isomiR analysis, enabling data sharing, reporting, comparative analyses, and benchmarking, while promoting the development of common miRNA methods focusing on downstream steps to miRNA detection, annotation, and quantification.

KW - file format

KW - isomiR

KW - microRNA

KW - reproducibility

KW - small RNA-seq

KW - standardization

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