SplicerAV: a tool for mining microarray expression data for changes in RNA processing.

Robinson TJ, Dinan MA, Dewhirst M, Garcia-Blanco MA, Pearson JL.

Citation

Robinson TJ, Dinan MA, Dewhirst M, Garcia-Blanco MA, Pearson JL. (2010) SplicerAV: a tool for mining microarray expression data for changes in RNA processing. BMC Bioinformatics 11:108.

Abstract

Using SplicerAV, we identified several hundred previously uncharacterized isoform changes induced by in vitro oncogene over-expression and revealed a previously unknown mechanism of EGFR activation in human mammary epithelial cells. We analyzed Affymetrix GeneChip data from over 400 human breast tumors in three independent studies, making this the largest clinical dataset analyzed for en masse changes in alternative mRNA processing. The capacity to detect RNA isoform changes in archival microarray data using SplicerAV allowed us to carry out the first analysis of isoform specific mRNA changes directly associated with cancer survival.