ArticleNucleic acids research2012
MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 229 papers.
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Who cites it
229 citing papers in PubMed.
- ZC3H14 phosphorylation is required for nuclear speckle assembly during zygotic splicing activation in mice.EMBO reports · 2026Article
- SRSF3 plays a key role in liver cancer sex disparity by facilitating hepatocyte expression of ERα and FOXA.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The essential chaperone DNAJC17 activates HSP70 to coordinate RNA splicing and G2-M progression.Scientific reports · 2026Article
- Dysregulation of alternative splicing patterns in the ovaries of reproductively aged mice.Reproduction (Cambridge, England) · 2026Article
- Azoospermia phenotype and scRNA-seq reveal hnRNPK as a factor essential for male germ cell development in mice.Nucleic acids research · 2026Article
- Butterfly brains change in morphology and in gene splicing patterns after brief pheromone exposure.BMC biology · 2026Article
- Unveiling the molecular impact of pulmonary embolism on the right ventricle: a multi-layer transcriptomic study in a porcine model.Molecular and cellular biochemistry · 2026Article
- Evolution of Plasticity in Response to Ethanol Between Recently Separated Populations ofEcology and evolution · 2026Article
- N6-methyladenosine regulation of mRNA translation is essential for early human erythropoiesis.bioRxiv : the preprint server for biology · 2025Article
- Differential Chromatin Accessibility, Gene Expression, and mRNA Splicing Between Developing Cochlear Inner and Outer Hair Cells.Journal of the Association for Research in Otolaryngology : JARO · 2025Article
- Viral Modulation of Host Splicing.Annual review of virology · 2025Review
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- Nuclear RNA cap-chaperones eIF4E and NCBP2 govern distinct fates for 1000s of mRNAs uncovering an unexpected regulatory point in gene expression.bioRxiv : the preprint server for biology · 2025Article
- Article
- Alternative mRNA splicing in anthracycline-induced cardiomyopathy - a COG-ALTE03N1 report.Cardio-oncology (London, England) · 2025Article
- Transcriptomic profiling of severe and critical COVID-19 patients reveals alterations in expression, splicing and polyadenylation.Scientific reports · 2025Article
- RNA splicing variants of the novel long non-coding RNA, CyKILR, possess divergent biological functions in non-small cell lung cancer.Molecular therapy. Nucleic acids · 2025Article
- Article
- Alternative splicing dysregulation across tissue and therapeutic approaches in a mouse model of myotonic dystrophy type 1.Molecular therapy. Nucleic acids · 2024Article
- GPATCH11 variants cause mis-splicing and early-onset retinal dystrophy with neurological impairment.Nature communications · 2024Article
169 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
Ultra-deep RNA sequencing has become a powerful approach for genome-wide analysis of pre-mRNA alternative splicing. We develop MATS (multivariate analysis of transcript splicing), a bayesian statistical framework for flexible hypothesis testing of differential alternative splicing patterns on RNA-Seq data. MATS uses a multivariate uniform prior to model the between-sample correlation in exon splicing patterns, and a Markov chain Monte Carlo (MCMC) method coupled with a simulation-based adaptive sampling procedure to calculate the P-value and false discovery rate (FDR) of differential alternative splicing. Importantly, the MATS approach is applicable to almost any type of null hypotheses of interest, providing the flexibility to identify differential alternative splicing events that match a given user-defined pattern. We evaluated the performance of MATS using simulated and real RNA-Seq data sets. In the RNA-Seq analysis of alternative splicing events regulated by the epithelial-specific splicing factor ESRP1, we obtained a high RT-PCR validation rate of 86% for differential exon skipping events with a MATS FDR of <10%. Additionally, over the full list of RT-PCR tested exons, the MATS FDR estimates matched well with the experimental validation rate. Our results demonstrate that MATS is an effective and flexible approach for detecting differential alternative splicing from RNA-Seq data.
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