ArticleFrontiers in genetics2011
Systematic Curation of miRBase Annotation Using Integrated Small RNA High-Throughput Sequencing Data for C. elegans and Drosophila.
Article in Frontiers in genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
32 citing papers in PubMed, 53 citations in OpenAlex.
- A subclass of small RNAs is encoded by exons of protein-coding genes.BMC genomics · 2025Article
- MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models.Nucleic acids research · 2025Article
- Rapid adaptation of cellular metabolic rate to the MicroRNA complements of mammals and its relevance to the evolution of endothermy.iScience · 2024Article
- Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine.Cell genomics · 2023Article
- MirGeneDB 2.1: toward a complete sampling of all major animal phyla.Nucleic acids research · 2022Article
- Barley Seeds miRNome Stability during Long-Term Storage and Aging.International journal of molecular sciences · 2021Article
- In Silico Analysis of Micro-RNA Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2021Article
- miR-632 Promotes Laryngeal Carcinoma Cell Proliferation, Migration, and Invasion Through Negative Regulation of GSK3β.Oncology research · 2020Article
- MirGeneDB 2.0: the metazoan microRNA complement.Nucleic acids research · 2020Article
- Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells.PloS one · 2020Article
- An estimate of the total number of true human miRNAs.Nucleic acids research · 2019Article
- Bias-minimized quantification of microRNA reveals widespread alternative processing and 3' end modification.Nucleic acids research · 2019Article
- Opportunities for microRNAs in the Crowded Field of Cardiovascular Biomarkers.Annual review of pathology · 2019Review
- miRBase: from microRNA sequences to function.Nucleic acids research · 2019Article
- miRge 2.0 for comprehensive analysis of microRNA sequencing data.BMC bioinformatics · 2018Article
- Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss.Genome biology and evolution · 2018Article
- miRDis: a Web tool for endogenous and exogenous microRNA discovery based on deep-sequencing data analysis.Briefings in bioinformatics · 2018Article
- Comparing miRNA structure of mirtrons and non-mirtrons.BMC genomics · 2018Article
- Genome-Wide Identification of Destruxin A-Responsive Immunity-Related MicroRNAs in Diamondback Moth,Frontiers in immunology · 2018Article
- Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
MicroRNAs (miRNAs) are a class of 20-23 nucleotide small RNAs that regulate gene expression post-transcriptionally in animals and plants. Annotation of miRNAs by the miRNA database (miRBase) has largely relied on computational approaches. As a result, many miRBase entries lack experimental validation, and discrepancies between miRBase annotation and actual miRNA sequences are often observed. In this study, we integrated the small RNA sequencing (smRNA-seq) datasets in Caenorhabditis elegans and Drosophila melanogaster and devised an analytical pipeline coupled with detailed manual inspection to curate miRNA annotation systematically in miRBase. Our analysis reveals 19 (17.0%) and 51 (31.3%) miRNAs entries with detectable smRNA-seq reads have mature sequence discrepancies in C. elegans and D. melanogaster, respectively. These discrepancies frequently occur either for conserved miRNA families whose mature sequences were predicted according to their homologous counterparts in other species or for miRNAs whose precursor miRNA (pre-miRNA) hairpins produce an abundance of multiple miRNA isoforms or variants. Our analysis shows that while Drosophila pre-miRNAs, on average, produce less than 60% accurate mature miRNA reads in addition to their 5' and 3' variant isoforms, the precision of miRNA processing in C. elegans is much higher, at over 90%. Based on the revised miRNA sequences, we analyzed expression patterns of the more conserved (MC) and less conserved (LC) miRNAs and found that, whereas MC miRNAs are often co-expressed at multiple developmental stages, LC miRNAs tend to be expressed specifically at fewer stages.
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Registered trials
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