A Bayesian model selection approach for identifying differentially expressed transcripts from RNA sequencing data.

Journal of the Royal Statistical Society. Series C, Applied Statistics
Panagiotis Papastamoulis, Magnus Rattray


Recent advances in molecular biology allow the quantification of the transcriptome and scoring transcripts as differentially or equally expressed between two biological conditions. Although these two tasks are closely linked, the available inference methods treat them separately: a primary model is used to estimate expression and its output is post processed by using a differential expression model. In the paper, both issues are simultaneously addressed by proposing the joint estimation of expression levels and differential expression: the unknown relative abundance of each transcript can either be equal or not between two conditions. A hierarchical Bayesian model builds on the BitSeq framework and the posterior distribution of transcript expression and differential expression is inferred by using Markov chain Monte Carlo sampling. It is shown that the model proposed enjoys conjugacy for fixed dimension variables; thus the full conditional distributions are analytically derived. Two samplers are constructed, a reversible jump Markov chain Monte Carlo sampler and a collapsed Gibbs sampler, and the latter is found to perform better. A cluster representation of the aligned reads to the transcriptome is introduced, allowing paralle...Continue Reading


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Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Jan 1, 1946·Proceedings of the Royal Society of London. Series A, Mathematical and Physical Sciences·H JEFFREYS
Apr 21, 2011·Algorithms for Molecular Biology : AMB·Marius NicolaeAlex Zelikovsky
Jun 1, 1984·IEEE Transactions on Pattern Analysis and Machine Intelligence·S Geman, D Geman
Dec 12, 2012·Nature Biotechnology·Cole TrapnellLior Pachter
Feb 23, 2013·Bioinformatics·Ning LengChristina Kendziorski
May 6, 2014·The Annals of Applied Statistics·David RossellAlmond Stöcker
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