Towards Reliable Isoform Quantification Using RNA-Seq Data

Background: In eukaryotes, alternative splicing often generates multiple splice variants from a single gene. Here weexplore the use of RNA sequencing (RNA-Seq) datasets to address the isoform quantification problem. Given a set of known splice variants, the goal is to estimate the relative abundance of the individual variants. Methods: Our method employs a linear models framework to estimate the ratios of known isoforms in a sample. A key feature of our method is that it takes into account the non-uniformity of RNA-Seq read positions along the targeted transcripts. Results: Preliminary tests indicate that the model performs well on both simulated and real data. In two publicly available RNA-Seq datasets, we identified several alternatively-spliced genes with switch-like, on/off expression properties, as well as a number of other genes that varied more subtly in isoform expression. In many cases, genes exhibiting differential expression of alternatively spliced transcripts were not dif...

• Type: Conference
• Year: 2009
• Where: BIBM
• Authors: Brian E. Howard, Steffen Heber
• Keywords: Alternative Splicing, BIBM 2009, Bioinformatics, Isoforms, Splice Variants