Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays

Background: Exon arrays provide a way to measure the expression of different isoforms of genes in an organism. Most of the procedures to deal with these arrays are focused on gene expression or on exon expression. Although the only biological analytes that can be properly assigned a concentration are transcripts, there are very few algorithms that focus on them. The reason is that previously developed summarization methods do not work well if applied to transcripts. In addition, gene structure prediction, i.e., the correspondence between probes and novel isoforms, is a field which is still unexplored. Results: We have modified and adapted a previous algorithm to take advantage of the special characteristics of the Affymetrix exon arrays. The structure and concentration of transcripts -some of them possibly unknown- in microarray experiments were predicted using this algorithm. Simulations showed that the suggested modifications improved both specificity (SP) and sensitivity (ST) of th...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Miguel A. Anton, Ander Aramburu, Angel Rubio
• Keywords: Algorithms, BMCBI 2007, BMCBI 2010, Exon, Isoform