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Bayesian estimation of differential transcript usage from RNA-seq data

Papastamoulis Panagiotis () and Rattray Magnus
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Papastamoulis Panagiotis: Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PL, UK
Rattray Magnus: Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK

Statistical Applications in Genetics and Molecular Biology, 2017, vol. 16, issue 5-6, 367-386

Abstract: Next generation sequencing allows the identification of genes consisting of differentially expressed transcripts, a term which usually refers to changes in the overall expression level. A specific type of differential expression is differential transcript usage (DTU) and targets changes in the relative within gene expression of a transcript. The contribution of this paper is to: (a) extend the use of cjBitSeq to the DTU context, a previously introduced Bayesian model which is originally designed for identifying changes in overall expression levels and (b) propose a Bayesian version of DRIMSeq, a frequentist model for inferring DTU. cjBitSeq is a read based model and performs fully Bayesian inference by MCMC sampling on the space of latent state of each transcript per gene. BayesDRIMSeq is a count based model and estimates the Bayes Factor of a DTU model against a null model using Laplace’s approximation. The proposed models are benchmarked against the existing ones using a recent independent simulation study as well as a real RNA-seq dataset. Our results suggest that the Bayesian methods exhibit similar performance with DRIMSeq in terms of precision/recall but offer better calibration of False Discovery Rate.

Keywords: alternative splicing; false discovery rate; Laplace approximation; MCMC; within gene transcript expression (search for similar items in EconPapers)
Date: 2017
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DOI: 10.1515/sagmb-2017-0005

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