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Minimal Standards for Reporting microRNA:Target Interactions
1Department of Animal Science, Biotechnical Faculty, University of Ljubljana , Domzale, Slovenia .
Abstract:
Epigenomics is one of the leading frontiers of postgenomics medicine. The challenges and prospects ahead in epigenomics are related not merely to technology innovation and clinical implementation but also to science communication. In this context, microRNAs (miRNAs) are an important part of the epigenomic regulatory machinery. As the number of publications reporting miRNA-target interactions (MTIs) is growing rapidly, there is an urgent need to standardize reporting. This study reports (1) an analysis of the published literature and databases reporting validated MTIs, and for the first time to the best of our knowledge (2) suggests a solution as a way forward, the minimum information required for MTI standard reporting. We retrieved the research reports from PubMed and Web of Science dating from 09/2006 to 01/2017 and downloaded information from DIANA-TarBase, miRecords, and miRTarBase. We evaluated the reporting and extracted MTI data, which we complemented with relevant genomic information. We suggest a standard minimum checklist for MTI reporting, consisting of seven pertinent data types: miRNA gene, target gene, species, experimental validation, sequence variants, associated phenotype, and additionally a PubMed identification (PMID) number in systematic reviews and meta-analyses. Our proposal reported here shall enable faster development of MTI databases and bioinformatics resources, and looking into the future, more efficient planning of experimental designs in the nascent field of epigenomics and its postgenomics applications.
Insights
Standardizing reporting for microRNA-target interactions (MTIs) is crucial for epigenomics research. This study proposes a minimum data checklist to improve MTI database development and experimental design in postgenomics medicine.
Area of Science:
- Epigenomics and Postgenomics Medicine
- Bioinformatics and Computational Biology
Background:
- Epigenomics is a key area in postgenomics medicine, with microRNAs (miRNAs) playing a vital role in its regulatory mechanisms.
- The rapid increase in publications on miRNA-target interactions (MTIs) necessitates standardized reporting for efficient data management and research.
- Current reporting lacks uniformity, hindering the development of comprehensive databases and bioinformatics resources.
Purpose of the Study:
- To analyze the reporting standards of published miRNA-target interactions (MTIs).
- To propose a minimum information standard for reporting MTIs to facilitate research and development.
- To address the science communication challenges in the growing field of epigenomics.
Main Methods:
- Literature retrieval from PubMed and Web of Science (2006-2017).
- Data extraction from MTI databases: DIANA-TarBase, miRecords, and miRTarBase.
- Evaluation of reported MTI data and integration with genomic information.
Main Results:
- Analysis revealed variability in the reporting of validated MTIs.
- A minimum reporting checklist comprising seven essential data types was developed.
- The checklist includes: miRNA gene, target gene, species, experimental validation, sequence variants, associated phenotype, and PMID for reviews.
Conclusions:
- The proposed MTI reporting standard will accelerate the development of MTI databases and bioinformatics tools.
- Implementation of this standard will enhance experimental design efficiency in epigenomics and postgenomics applications.
- Standardization is essential for advancing the field of epigenomics and its clinical translation.