Journal article
rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data
Proceedings of the National Academy of Sciences - PNAS, Vol.111(51), pp.E5593-E5601
12/23/2014
DOI: 10.1073/pnas.1419161111
PMCID: PMC4280593
PMID: 25480548
Abstract
Ultra-deep RNA sequencing (RNA-Seq) has become a powerful approach for genome-wide analysis of pre-mRNA alternative splicing. We previously developed multivariate analysis of transcript splicing (MATS), a statistical method for detecting differential alternative splicing between two RNA-Seq samples. Here we describe a new statistical model and computer program, replicate MATS (rMATS), designed for detection of differential alternative splicing from replicate RNA-Seq data. rMATS uses a hierarchical model to simultaneously account for sampling uncertainty in individual replicates and variability among replicates. In addition to the analysis of unpaired replicates, rMATS also includes a model specifically designed for paired replicates between sample groups. The hypothesis-testing framework of rMATS is flexible and can assess the statistical significance over any user-defined magnitude of splicing change. The performance of rMATS is evaluated by the analysis of simulated and real RNA-Seq data. rMATS outperformed two existing methods for replicate RNA-Seq data in all simulation settings, and RT-PCR yielded a high validation rate (94%) in an RNA-Seq dataset of prostate cancer cell lines. Our data also provide guiding principles for designing RNA-Seq studies of alternative splicing. We demonstrate that it is essential to incorporate biological replicates in the study design. Of note, pooling RNAs or merging RNA-Seq data from multiple replicates is not an effective approach to account for variability, and the result is particularly sensitive to outliers. The rMATS source code is freely available at rnaseq-mats.sourceforge.net/. As the popularity of RNA-Seq continues to grow, we expect rMATS will be useful for studies of alternative splicing in diverse RNA-Seq projects.
Details
- Title: Subtitle
- rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data
- Creators
- Shihao Shen - Departments of Microbiology, Immunology, & Molecular Genetics andJuw Won Park - Departments of Microbiology, Immunology, & Molecular Genetics andZhi-xiang Lu - Departments of Microbiology, Immunology, & Molecular Genetics andLan Lin - Departments of Microbiology, Immunology, & Molecular Genetics andMichael D Henry - Departments of Molecular Physiology and Biophysics and Pathology, University of Iowa, Iowa City, IA 52242Ying Nian Wu - Statistics, University of California, Los Angeles, CA 90095; andQing Zhou - Statistics, University of California, Los Angeles, CA 90095; andYi Xing - Departments of Microbiology, Immunology, & Molecular Genetics and yxing@ucla.edu
- Resource Type
- Journal article
- Publication Details
- Proceedings of the National Academy of Sciences - PNAS, Vol.111(51), pp.E5593-E5601
- DOI
- 10.1073/pnas.1419161111
- PMID
- 25480548
- PMCID
- PMC4280593
- NLM abbreviation
- Proc Natl Acad Sci U S A
- ISSN
- 0027-8424
- eISSN
- 1091-6490
- Publisher
- National Academy of Sciences; United States
- Grant note
- R01 GM088342 / NIGMS NIH HHS R01NS076631 / NINDS NIH HHS R01 ES024995 / NIEHS NIH HHS R01GM105431 / NIGMS NIH HHS R01 NS076631 / NINDS NIH HHS R01GM088342 / NIGMS NIH HHS R01 GM105431 / NIGMS NIH HHS R01ES024995 / NIEHS NIH HHS
- Language
- English
- Date published
- 12/23/2014
- Academic Unit
- Molecular Physiology and Biophysics; Pathology; Radiation Oncology; Urology
- Record Identifier
- 9984025586702771
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