ArticleNature communications2021
MOCCASIN: a method for correcting for known and unknown confounders in RNA splicing analysis.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- The impact of read depth and read length on RNA-seq splicing analysis.RNA (New York, N.Y.) · 2026Article
- The exon junction complex coordinates the cotranscriptional inclusion of blocks of neighboring exons.Genes & development · 2026Article
- A deep dive into statistical modeling of RNA splicing QTLs reveals variants that explain neurodegenerative disease.American journal of human genetics · 2025Article
- Integrative analysis of RNA binding proteins identifies DDX55 as a novel regulator of 3'UTR isoform diversity.Genome biology · 2025Article
- Multi-region brain transcriptomic analysis of amyotrophic lateral sclerosis reveals widespread RNA alterations and substantial cerebellum involvement.Molecular neurodegeneration · 2025Article
- Steering research on mRNA splicing in cancer towards clinical translation.Nature reviews. Cancer · 2024Review
- Trametinib Sensitivity is Defined by a Myeloid Differentiation Profile in Acute Myeloid Leukemia.Drugs in R&D · 2024Article
- BEERS2: RNA-Seq simulation through high fidelity in silico modeling.Briefings in bioinformatics · 2024Article
- Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy.Science translational medicine · 2024Article
- MAJIQlopedia: an encyclopedia of RNA splicing variations in human tissues and cancer.Nucleic acids research · 2024Article
- Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis.Briefings in bioinformatics · 2023Review
- LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways.Nature communications · 2023Article
- Integrated transcriptome landscape of ALS identifies genome instability linked to TDP-43 pathology.Nature communications · 2023Article
- RNA splicing analysis using heterogeneous and large RNA-seq datasets.Nature communications · 2023Article
- A Bayesian model for unsupervised detection of RNA splicing based subtypes in cancers.Nature communications · 2023Article
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9 authors.
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Abstract
The effects of confounding factors on gene expression analysis have been extensively studied following the introduction of high-throughput microarrays and subsequently RNA sequencing. In contrast, there is a lack of equivalent analysis and tools for RNA splicing. Here we first assess the effect of confounders on both expression and splicing quantifications in two large public RNA-Seq datasets (TARGET, ENCODE). We show quantification of splicing variations are affected at least as much as those of gene expression, revealing unwanted sources of variations in both datasets. Next, we develop MOCCASIN, a method to correct the effect of both known and unknown confounders on RNA splicing quantification and demonstrate MOCCASIN's effectiveness on both synthetic and real data. Code, synthetic and corrected datasets are all made available as resources.
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