ArticleBioinformatics (Oxford, England)2020
Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 57 citations in OpenAlex.
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- PARiS: Probabilistic Assignment and Repartitioning of isomiR Sequences: A data-driven method for denoising isomiR read count data.bioRxiv : the preprint server for biology · 2026Article
- Serum and serum-derived extracellular vesicle microRNA signatures linked to neurodevelopmental processes in central precocious puberty.Frontiers in endocrinology · 2026Article
- IsomiR stoichiometry changes as disease biomarkers.Molecular therapy. Nucleic acids · 2025Article
- Charting the equine miRNA landscape: An integrated pipeline and browser for annotating, quantifying, and visualizing expression.PLoS genetics · 2025Article
- HDACs and Their Inhibitors on Post-Translational Modifications: The Regulation of Cardiovascular Disease.Cells · 2025Review
- Re-Analyses of Samples From Amyotrophic Lateral Sclerosis Patients and Controls Identify Many Novel Small RNAs With Diagnostic And Prognostic Potential.Molecular neurobiology · 2025Article
- Combinational regenerative inductive effect of bio-adhesive hybrid hydrogels conjugated with hiPSC-derived myofibers and its derived EVs for volumetric muscle regeneration.Bioactive materials · 2025Article
- IL-1β Induces Human Endothelial Surface Expression of IL-15 by Relieving let-7c-3p Suppression of Protein Translation.Journal of immunology (Baltimore, Md. : 1950) · 2024Article
- sRNAflow: A Tool for the Analysis of Small RNA-Seq Data.Non-coding RNA · 2024Article
- MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs).Nucleic acids research · 2024Article
- 3'IsomiR Species Composition Affects Reliable Quantification of miRNA/isomiR Variants by Poly(A) RT-qPCR: Impact on Small RNA-Seq Profiling Validation.International journal of molecular sciences · 2023Article
- Circular RNA circEMB promotes osteosarcoma progression and metastasis by sponging miR-3184-5p and regulating EGFR expression.Biomarker research · 2023Article
- Hepatoprotective effects of sevoflurane against hepatic ischemia-reperfusion injury by regulating microRNA-124-3p-mediated TRAF3/CREB axis.Cell death discovery · 2022Article
- FishmiRNA: An Evolutionarily Supported MicroRNA Annotation and Expression Database for Ray-Finned Fishes.Molecular biology and evolution · 2022Article
- Article
- Circulating miRNA repertoire as a biomarker of metabolic and reproductive states in rainbow trout.BMC biology · 2021Article
- miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline.NAR genomics and bioinformatics · 2021Article
- Evolution after Whole-Genome Duplication: Teleost MicroRNAs.Molecular biology and evolution · 2021Article
- IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets.Bioinformatics (Oxford, England) · 2021Article
Corrections and comments
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Authors and funding
22 authors at 12 institutions in 5 countries.
Funding
Abstract
motivationMicroRNAs (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.
resultsTo 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. AVAILABILITY AND IMPLEMENTATION: https://github.com/miRTop/mirGFF3/ and https://github.com/miRTop/mirtop. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.