Isoform Detection from RNA-seq with Restriction Enzyme Fragmentation

• Activity Number: 157
• Type: Topic Contributed
• Date/Time: Monday, August 2, 2010 : 10:30 AM to 12:20 PM
• Sponsor: Biometrics Section
• Author(s): Naomi S. Altman*+ and Qingyu Wang and Aleksandra B. Slavkovic and Vishesh Karwa
• Companies: Penn State and Penn State and Penn State and Penn State
• Keywords: gene expression ; RNA-seq ; isoform ; bioinformatics ; differential expression

Abstract

Genes in complex organisms may encode multiple mRNAs, called isoforms which result in different proteins. Isoform expression is often more relevant than gene expression. The advent of ultra-high throughput sequencing technology has made it possible to directly sequence large numbers of RNA fragments, obtaining a direct measure RNA abundance. Restriction enzyme fragmentation reliably produces a single sequenced fragment per RNA, providing a direct measure of gene expression from tag counts. However, since each restriction site can belong to multiple isoforms, the counts must be partitioned among the isoforms to derive accurate isoform counts. We combine a model for fragmentation with methodology for contingency table analysis to estimate isoform abundance taking into consideration differing probabilities of restriction failure for each isoform.