ArticleBMC bioinformatics2018
miRBaseConverter: an R/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers, 1 of them a synthesis that pooled it.
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Who cites it
59 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Potential contribution of age-related and methodological factors to limited reproducibility in autism spectrum disorder blood miRNA biomarker studies: an exploratory meta-analysis.Scientific reports · 2026Pooled it
- Circulating extracellular vesicle microRNAs mediate immune modulation of social behavior in male mice.Nature communications · 2026Article
- A Narrative Review on Integrative Bioinformatics Approaches for microRNA Research in Familial Mediterranean Fever: Current Insights and Future Directions.Health science reports · 2026Article
- Site- and cell-type-specific miRNA and mRNA genes and networks across the cortex, striatum, and hypothalamus.Communications biology · 2025Article
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- Multi-omics analysis in inclusion body myositis identifies mir-16 responsible for HLA overexpression.Orphanet journal of rare diseases · 2025Article
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- Characterizing the pan-cancer role of exosomal miRNAs in metastasis across cancers.Computational and structural biotechnology journal · 2025Article
- Exosomes loaded with the anti-cancer molecule mir-1-3p inhibit intrapulmonary colonization and growth of human esophageal squamous carcinoma cells.Journal of translational medicine · 2024Article
- Discovery of miRNA-mRNA regulatory networks in glioblastoma reveals novel insights into tumor microenvironment remodeling.Scientific reports · 2024Article
- Quantitative design of cell type-specific mRNA stability from microRNA expression data.bioRxiv : the preprint server for biology · 2024Article
- microRNA profile of endometrial cancer from Indian patients-identification of potential biomarkers for prognosis.Biochemistry and biophysics reports · 2024Article
- Characterizing the role of exosomal miRNAs in metastasis.bioRxiv : the preprint server for biology · 2024Article
- A dynamic microRNA profile that tracks a chemotherapy resistance phenotype in osteosarcoma. Implications for novel therapeutics.medRxiv : the preprint server for health sciences · 2024Article
- A Systematic Review and Meta-Analysis of microRNA Profiling Studies in Chronic Kidney Diseases.Non-coding RNA · 2024Review
- miRNA signatures underlie chemoresistance in the gemcitabine-resistant pancreatic ductal adenocarcinoma cell line MIA PaCa-2 GR.Frontiers in genetics · 2024Article
- Integrative analysis of mRNA and miRNA expression profiles and somatic variants in oxysterol signaling in early-stage luminal breast cancer.Molecular oncology · 2023Article
- A Diagnostic Classifier Based on Circulating miRNA Pairs for COPD Using a Machine Learning Approach.Diagnostics (Basel, Switzerland) · 2023Article
- The 8q24 region hosts miRNAs altered in biospecimens of colorectal and bladder cancer patients.Cancer medicine · 2023Article
- An evaluation of gastric adenocarcinoma-associated CircRNAs based on microarray meta-analysis and ceRNA networks.Translational oncology · 2023Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundmiRBase is the primary repository for published miRNA sequence and annotation data, and serves as the "go-to" place for miRNA research. However, the definition and annotation of miRNAs have been changed significantly across different versions of miRBase. The changes cause inconsistency in miRNA related data between different databases and articles published at different times. Several tools have been developed for different purposes of querying and converting the information of miRNAs between different miRBase versions, but none of them individually can provide the comprehensive information about miRNAs in miRBase and users will need to use a number of different tools in their analyses.
resultsWe introduce miRBaseConverter, an R package integrating the latest miRBase version 22 available in Bioconductor to provide a suite of functions for converting and retrieving miRNA name (ID), accession, sequence, species, version and family information in different versions of miRBase. The package is implemented in R and available under the GPL-2 license from the Bioconductor website ( http://bioconductor.org/packages/miRBaseConverter/ ). A Shiny-based GUI suitable for non-R users is also available as a standalone application from the package and also as a web application at http://nugget.unisa.edu.au:3838/miRBaseConverter . miRBaseConverter has a built-in database for querying miRNA information in all species and for both pre-mature and mature miRNAs defined by miRBase. In addition, it is the first tool for batch querying the miRNA family information. The package aims to provide a comprehensive and easy-to-use tool for miRNA research community where researchers often utilize published miRNA data from different sources.
conclusionsThe Bioconductor package miRBaseConverter and the Shiny-based web application are presented to provide a suite of functions for converting and retrieving miRNA name, accession, sequence, species, version and family information in different versions of miRBase. The package will serve a wide range of applications in miRNA research and could provide a full view of the miRNAs of interest.
Indexed as
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What OpenQuestion holds
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.