Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays

Background: Alternative splicing (AS) is a process which generates several distinct mRNA isoforms from the same gene by splicing different portions out of the precursor transcript. Due to the (patho-)physiological importance of AS, a complete inventory of AS is of great interest. While this is in reach for human and mammalian model organisms, our knowledge of AS in plants has remained more incomplete. Experimental approaches for monitoring AS are either based on transcript sequencing or rely on hybridization to DNA microarrays. Among the microarray platforms facilitating the discovery of AS events, tiling arrays are well-suited for identifying intron retention, the most prevalent type of AS in plants. However, analyzing tiling array data is challenging, because of high noise levels and limited probe coverage. Results: In this work, we present a novel method to detect intron retentions (IR) and exon skips (ES) from tiling arrays. While statistical tests have typically been proposed for...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Johannes Eichner, Georg Zeller, Sascha Laubinger, Gunnar Rätsch
• Keywords: Artificial Intelligence, BMCBI 2011, Intron Retentions, IR Events, TAIR Annotation