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

Background: Over the past two decades more than fifty thousand unique clinical and biological samples have been assayed using the Affymetrix HG-U133 and HG-U95 GeneChip microarray platforms. This substantial repository has been used extensively to characterize changes in gene expression between biological samples, but has not been previously mined en masse for changes in mRNA processing. We explored the possibility of using HG-U133 microarray data to identify changes in alternative mRNA processing in several available archival datasets. Results: Data from these and other gene expression microarrays can now be mined for changes in transcript isoform abundance using a program described here, SplicerAV. Using in vivo and in vitro breast cancer microarray datasets, SplicerAV was able to perform both gene and isoform specific expression profiling within the same microarray dataset. Our reanalysis of Affymetrix U133 plus 2.0 data generated by in vitro over-expression of HRAS, E2F3, beta-cat...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Timothy J. Robinson, Michaela A. Dinan, Mark Dewhirst, Mariano A. Garcia-Blanco, James L. Pearson
• Keywords: BMCBI 2010, Isoform, Isoform Changes, MRNA