ArticleNucleic acids research2016
Accurate detection for a wide range of mutation and editing sites of microRNAs from small RNA high-throughput sequencing profiles.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it, 48 citations in OpenAlex.
- A Systematic Review of Common and Brain-Disease-Specific RNA Editing Alterations Providing Novel Insights into Neurological and Neurodegenerative Disease Manifestations.Biomolecules · 2022Pooled it
- MicroRNA‑microbiome cross‑kingdom networks drive inflammatory bowel disease through dynamic regulatory ecosystems (Review).International journal of molecular medicine · 2026Review
- Characterizing miRNA editing patterns in 5 types of cells using single-cell small RNA sequencing data.Frontiers in bioinformatics · 2026Article
- Intrauterine Growth-Restricted Pig-Associated Testicular Transcriptome Analysis Reveals microRNA-mRNA Regulatory Networks.Animals : an open access journal from MDPI · 2025Article
- Characterization and Function Analysis of miRNA Editing during Fat Deposition in Chinese Indigenous Ningxiang Pigs.Veterinary sciences · 2024Article
- Improved lung cancer classification by employing diverse molecular features of microRNAs.Heliyon · 2024Article
- Differential Expression of miRNAs, lncRNAs, and circRNAs between Ovaries and Testes in Common Carp (Cells · 2023Article
- Identification of microRNA editing sites in clear cell renal cell carcinoma.Scientific reports · 2023Article
- Deciphering the enigma of RNA editing in the ATP1_alpha subunit of ATP synthase inSaudi journal of biological sciences · 2023Article
- Article
- Review
- Genetic architecture of microRNA expression and its link to complex diseases in the Japanese population.Human molecular genetics · 2022Article
- MicroRNA editing patterns in Huntington's disease.Scientific reports · 2022Article
- Genome-Wide Analysis of microRNAs Identifies the Lipid Metabolism Pathway to Be a Defining Factor in Adipose Tissue From Different Sheep.Frontiers in veterinary science · 2022Article
- Characterizing microRNA editing and mutation sites in Autism Spectrum Disorder.Frontiers in molecular neuroscience · 2022Article
- Identification of microRNA editing sites in three subtypes of leukemia.Frontiers in molecular biosciences · 2022Article
- MiREDiBase, a manually curated database of validated and putative editing events in microRNAs.Scientific data · 2021Article
- Review
- Editing and Chemical Modifications on Non-Coding RNAs in Cancer: A New Tale with Clinical Significance.International journal of molecular sciences · 2021Review
- Human Brain Shows Recurrent Non-Canonical MicroRNA Editing Events Enriched for Seed Sequence with Possible Functional Consequence.Non-coding RNA · 2020Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Various types of mutation and editing (M/E) events in microRNAs (miRNAs) can change the stabilities of pre-miRNAs and/or complementarities between miRNAs and their targets. Small RNA (sRNA) high-throughput sequencing (HTS) profiles can contain many mutated and edited miRNAs. Systematic detection of miRNA mutation and editing sites from the huge volume of sRNA HTS profiles is computationally difficult, as high sensitivity and low false positive rate (FPR) are both required. We propose a novel method (named MiRME) for an accurate and fast detection of miRNA M/E sites using a progressive sequence alignment approach which refines sensitivity and improves FPR step-by-step. From 70 sRNA HTS profiles with over 1.3 billion reads, MiRME has detected thousands of statistically significant M/E sites, including 3'-editing sites, 57 A-to-I editing sites (of which 32 are novel), as well as some putative non-canonical editing sites. We demonstrated that a few non-canonical editing sites were not resulted from mutations in genome by integrating the analysis of genome HTS profiles of two human cell lines, suggesting the existence of new editing types to further diversify the functions of miRNAs. Compared with six existing studies or methods, MiRME has shown much superior performance for the identification and visualization of the M/E sites of miRNAs from the ever-increasing sRNA HTS profiles.
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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.