2414–2425 Nucleic Acids Research, 2012, Vol. 40, No. 6 doi:10.1093/nar/gkr1110 Published online 28 November 2011 Gene Array Analyzer: alternative usage of gene arrays to study alternative splicing events Pascal Gellert1, Mizue Teranishi1, Katharina Jenniches1, Piera De Gaspari1, David John 1 , Karsten grosse Kreymborg1,2, Thomas Braun1,* and Shizuka Uchida1,* 1Max-Planck Institute for Heart and Lung Research, Ludwigstrasse 43, 61231 Bad Nauheim and 2Pediatric Heart Center, University of Giessen and Marburg, Feulgenstrasse 12, 35390 Giessen, Germany Received August 2, 2011; Revised October 30, 2011; Accepted November 5, 2011 ABSTRACT Exon arrays are regularly used to analyze differential splicing events. GeneChip Gene 1.0 ST Arrays (gene arrays) manufactured by Affymetrix, Inc. are primarily used to determine expression levels of transcripts, although their basic design is rather similar to GeneChip Exon 1.0 ST Arrays (exon arrays). Here, we show that the newly developed Gene Array Analyzer (GAA), which evolved from our previously published Exon Array Analyzer (EAA), enables economic and user-friendly analysis of alternative splicing events using gene arrays. To demonstrate the applicability of GAA, we profiled alternative splicing events during embryonic heart development. In addition, we found that numerous developmental splicing events are also activated under pathological conditions. We reason that the usage of GAA considerably expands the analysis of gene expression based on gene arrays and supplies an additional level of information without further costs and with only little effort. INTRODUCTION Alternative splicing (AS) is a post-transcriptional process based on the joining of exons of a gene in different com- binations to generate various isoforms from a single gene. It has been shown that most genes have at least one alternative isoform (1), which can be expressed in a tissue, development or sex-speciﬁc manner and fulﬁll dif- ferent or even opposing functions (1–3). Traditional microarrays are not capable of detecting alternative spliced isoforms, since their probes target only small regions at the 30-end of genes (30 arrays). In contrast, whole-transcript arrays, such as exon arrays from Affymetrix, Inc. (GeneChip Exon 1.0 ST Array), contain probe sets (consisting of up to four probes) rep- resenting every exon. Additional probe sets are provided on exon arrays to allow identiﬁcations of internal splice sites, retaining introns or putative exons. This approach allows the detection of over 1.4 million expressed sequences. Recently, GeneChip Gene 1.0 ST Array (gene array) was released by Affymetrix, Inc. This microarray platform was designed to measure gene expressions rather than expressions of single exons. However, gene arrays are very similar to exon arrays in respect to the hybridization protocol and coverage of annotated genes (4,5). The majority of probe sets present on gene arrays is identical to probes of high-quality annotation (core annotation) of exon arrays, but probe sets for puta- tive exons and genes are not integrated into gene arrays (Figure 1A). Additionally, probe sets on gene arrays consist of only two instead of four probes (Figure 1B). Previous studies indicate that both exon and gene arrays correlate well to 30 arrays in respect to gene expressions [correlation of 0.80 as reported by (7)] and very highly to each other at both gene and exon levels [R = 0.94 and R = 0.91, respectively as reported by (8)]. This implies that gene arrays are also capable of detecting differentially expressed exons, but the coverage of individual exons is limited compared with exon arrays (9). Although gene arrays are more affordable than exon arrays or deep sequencing, their intended usage focuses solely at the gene expression level, which leaves additional information contained in them untouched. *To whom correspondence should be addressed. Tel: +49 6032 705 1107; Fax: +49 6032 705 1104; Email: shizuka.uchida@mpi-bn.mpg.de Correspondence may also be addressed to Thomas Braun. Tel: +49 6032 705 1101; Fax: +49 6032 705 1104; Email: thomas.braun@mpi-bn.mpg.de The authors wish it to be known that, in their opinion, the ﬁrst two authors should be regarded as joint First Authors. The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.