AUTHOR=Bhattacharjee Madhuchhanda , Gupta Ravi , Davuluri Ramana TITLE=Estimation of Gene Expression at Isoform Level from mRNA-Seq Data by Bayesian Hierarchical Modeling JOURNAL=Frontiers in Genetics VOLUME=3 YEAR=2012 URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2012.00239 DOI=10.3389/fgene.2012.00239 ISSN=1664-8021 ABSTRACT=
mRNA-Seq is a precise and highly reproducible technique for measurement of transcripts levels and yields sequence information of a transcriptome at a single nucleotide base-level thus enabling us to determine splice junctions and alternative splicing events with high confidence. Often analysis of mRNA-Seq data does not attempt to quantify the expressions at isoform level. In this paper our objective would be use the mRNA-Seq data to infer expression at isoform level, where splicing patterns of a gene is assumed to be known. A Bayesian latent variable based modeling framework is proposed here, where the parameterization enables us to infer at various levels. For example, expression variability of an isoform across different conditions; the model parameterization also allows us to carry out two-sample comparisons, e.g., using a Bayesian