ArticleBioinformatics (Oxford, England)2020
Statistical inference of differential RNA-editing sites from RNA-sequencing data by hierarchical modeling.
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 25 papers.
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Who cites it
25 citing papers in PubMed, 35 citations in OpenAlex.
- A dual role of EZH2 in regulating A-to-I RNA editing and mRNA stability through ADAR.Nature communications · 2026Article
- Integration of RNA Editing into Multiomics Machine Learning Models for Predicting Drug Responses in Breast Cancer Patients.Biomedicines · 2026Article
- Allele-specific splicing modulates protein isoforms and Alzheimer's risk.bioRxiv : the preprint server for biology · 2026Article
- RNA-seq variants reveal distinct patterns in the aging epitranscriptome: an in-depth analysis of age-matched Alzheimer's Disease patients and a cognitively normal cohort.bioRxiv : the preprint server for biology · 2026Article
- Allele-specific alternative polyadenylation links noncoding genetic variation to Alzheimer's disease risk.bioRxiv : the preprint server for biology · 2026Article
- RNA editing in cardiovascular health and disease.Communications biology · 2026Review
- A dynamic RNA editing landscape in porcine spleen highlights a post-transcriptional mechanism for immune maturation.Molecular genetics and genomics : MGG · 2026Article
- RNA editing: an emerging frontier in cancer therapy - explorations, opportunities, and challenges.International journal of surgery (London, England) · 2026Article
- In-depth analysis of the RNA editing landscape in intracranial aneurysms and its potential role in alternative splicing.Computational and structural biotechnology journal · 2025Article
- Integration of RNA Editing with Multiomics Data Improves Machine Learning Models for Predicting Drug Responses in Breast Cancer Patients.Research square · 2024Article
- LoDEI: a robust and sensitive tool to detect transcriptome-wide differential A-to-I editing in RNA-seq data.Nature communications · 2024Article
- ADAR-Mediated A>I(G) RNA Editing in the Genotoxic Drug Response of Breast Cancer.International journal of molecular sciences · 2024Review
- Article
- 2'-O-methylation at internal sites on mRNA promotes mRNA stability.Molecular cell · 2024Article
- Temporal landscape and translational regulation of A-to-I RNA editing in mouse retina development.BMC biology · 2024Article
- A Comprehensive Analysis of the Effect of A>I(G) RNA-Editing Sites on Genotoxic Drug Response and Progression in Breast Cancer.Biomedicines · 2024Article
- Global characterization of RNA editing in genetic regulation of multiple ovarian cancer subtypes.Molecular therapy. Nucleic acids · 2024Article
- RNA editing regulates host immune response and T cell homeostasis in SARS-CoV-2 infection.PloS one · 2024Article
- Article
- Single-Cell Analysis in Lung Adenocarcinoma Implicates RNA Editing in Cancer Innate Immunity and Patient Prognosis.Cancer research · 2023Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
motivationRNA-sequencing (RNA-seq) enables global identification of RNA-editing sites in biological systems and disease. A salient step in many studies is to identify editing sites that statistically associate with treatment (e.g. case versus control) or covary with biological factors, such as age. However, RNA-seq has technical features that incumbent tests (e.g. t-test and linear regression) do not consider, which can lead to false positives and false negatives.
resultsIn this study, we demonstrate the limitations of currently used tests and introduce the method, RNA-editing tests (REDITs), a suite of tests that employ beta-binomial models to identify differential RNA editing. The tests in REDITs have higher sensitivity than other tests, while also maintaining the type I error (false positive) rate at the nominal level. Applied to the GTEx dataset, we unveil RNA-editing changes associated with age and gender, and differential recoding profiles between brain regions. AVAILABILITY AND IMPLEMENTATION: REDITs are implemented as functions in R and freely available for download at https://github.com/gxiaolab/REDITs. The repository also provides a code example for leveraging parallelization using multiple cores.
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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.