2424 Nucleic Acids Research, 2012, Vol. 40, No. 6 of individual exons in the genome. We reason that GAA is a valuable tool for biologists and adds another layer of analysis to gene array without additional costs. The web interface of GAA is easy to use, requires no set up and is freely available at http://GAA.mpi-bn.mpg.de. ACCESSION NUMBERS Gene Expression Omnibus: GSE30429 and GSE33183. SUPPLEMENTARY DATA Supplementary Data are available at NAR Online: Supplementary Figures 1–4, Supplementary Tables 1–8. ACKNOWLEDGEMENTS We thank Dr Petra Uchida for her valuable advice and comments on this article, and Silvia Thomas for help with gene array experiments. S.U. conceived of the project. P.G. developed GAA. P.G. and D.J. performed computa- tional analysis. M.T. performed gene array experiments. M.T., P.D.-G. and K.J. performed biological experiments. K.gK. operated cardiac hypertrophy mice and provided samples. T.B. provided general guidance. S.U., P.G., M.T. and T.B. drafted the manuscript. All authors read and approved the ﬁnal manuscript. FUNDING Excellence Cluster Cardio-Pulmonary System (ECCPS); LOEWE Center for Cell and Gene Therapy (to S.U.); by fellowships of the International Max Planck Research School for Heart and Lung Research (IMPRS-HLR) (to K.J. and P.D.G.); Max-Planck-Society; DFG (Br1416); Excellence Initiative ‘Cardiopulmonary System’ (to T.B.); University of Giessen-Marburg Lung Center (UGMLC); Cell and Gene Therapy Center (CGT) sup- ported by the HMWK. Funding for open access charge: Max-Plank-Society. Conﬂict of interest statement. None declared. REFERENCES 1. Wang,E.T., Sandberg,R., Luo,S., Khrebtukova,I., Zhang,L., Mayr,C., Kingsmore,S.F., Schroth,G.P. and Burge,C.B. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature, 456, 470–476. 2. Blekhman,R., Marioni,J.C., Zumbo,P., Stephens,M. and Gilad,Y. (2009) Sex-speciﬁc and lineage-speciﬁc alternative splicing in primates. Genome Res., 20, 180–189. 3. Stetefeld,J. and Ruegg,M. (2005) Structural and functional diversity generated by alternative mRNA splicing. Trends Biochem. Sci., 30, 515–521. 4. Affymetrix Inc. (2009) GeneChip Exon Array System for Human, Mouse, and Rat. www.affymetrix.com. 5. Affymetrix Inc. (2007) GeneChip Gene 1.0 ST Array System for Human, Mouse and Rat. www.affymetrix.com. 6. Goecks,J., Nekrutenko,A. and Taylor,J. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86. 7. Robinson,M.D. and Speed,T.P. (2007) A comparison of Affymetrix gene expression arrays. BMC Bioinformatics, 8, 449. 8. Ha,K.C., Coulombe-Huntington,J. and Majewski,J. (2009) Comparison of Affymetrix Gene Array with the Exon Array shows potential application for detection of transcript isoform variation. BMC Genomics, 10, 519. 9. Robinson,M.D. and Speed,T.P. (2009) Differential splicing using whole-transcript microarrays. BMC Bioinformatics, 10, 156. 10. Gellert,P., Uchida,S. and Braun,T. (2009) Exon Array Analyzer: a web interface for Affymetrix exon array analysis. Bioinformatics, 25, 3323–3324. 11. Clark,T., Schweitzer,A., Chen,T., Staples,M., Lu,G., Wang,H., Williams,A. and Blume,J. (2007) Discovery of tissue-speciﬁc exons using comprehensive human exon microarrays. Genome Biol., 8, R64. 12. Gardina,P.J., Clark,T.A., Shimada,B., Staples,M.K., Yang,Q., Veitch,J., Schweitzer,A., Awad,T., Sugnet,C., Dee,S. et al. (2006) Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics, 7, 325. 13. Revil,T., Gaffney,D., Dias,C., Majewski,J. and Jerome- Majewska,L.A. (2010) Alternative splicing is frequent during early embryonic development in mouse. BMC Genomics, 11, 399. 14. Thorsen,K., Mansilla,F., Schepeler,T., ster,B., Rasmussen,M.H., Dyrskjt,L., Karni,R., Akerman,M., Krainer,A.R., Laurberg,S. et al. (2011) Alternative splicing of SLC39A14 in colorectal cancer is regulated by the Wnt pathway. Mol. Cell Proteomics, 10, M110.002998. 15. Bemmo,A., Benovoy,D., Kwan,T., Gaffney,D.J., Jensen,R.V. and Majewski,J. (2008) Gene expression and isoform variation analysis using Affymetrix Exon Arrays. BMC Genomics, 9, 529. 16. Affymetrix Inc. (2008) Identifying and validating alternative splicing events. www.affymetrix.com. 17. Smyth,G.K. (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol., 3, Article3. 18. Shah,S.H. and Pallas,J.A. (2009) Identifying differential exon splicing using linear models and correlation coefﬁcients. BMC Bioinformatics, 10, 26. 19. Kent,W.J., Sugnet,C.W., Furey,T.S., Roskin,K.M., Pringle,T.H., Zahler,A.M. and Haussler,D. (2002) The human genome browser at UCSC. Genome Res., 12, 996–1006. 20. Thierry-Mieg,D. and Thierry-Mieg,J. (2006) AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol., 7(Suppl. 1), S12.1–14. 21. Foissac,S. and Sammeth,M. (2007) ASTALAVISTA: dynamic and ﬂexible analysis of alternative splicing events in custom gene datasets. Nucleic Acids Res., 35, W297–W299. 22. Irizarry,R.A., Hobbs,B., Collin,F., Beazer-Barclay,Y.D., Antonellis,K.J., Scherf,U. and Speed,T.P. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249–264. 23. Zweigerdt,R., Burg,M., Willbold,E., Abts,H. and Ruediger,M. (2003) Generation of conﬂuent cardiomyocyte monolayers derived from embryonic stem cells in suspension: a cell source for new therapies and screening strategies. Cytotherapy, 5, 399–413. 24. Saeed,A.I., Bhagabati,N.K., Braisted,J.C., Liang,W., Sharov,V., Howe,E.A., Li,J., Thiagarajan,M., White,J.A. and Quackenbush,J. (2006) TM4 microarray software suite. Methods Enzymol., 411, 134–193. 25. Sto¨ ver,B.C. and Mu¨ ller,K.F. (2010) TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics, 11, 7. 26. Castle,J.C., Zhang,C., Shah,J.K., Kulkarni,A.V., Kalsotra,A., Cooper,T.A. and Johnson,J.M. (2008) Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat. Genet., 40, 1416–1425. 27. Kalsotra,A., Xiao,X., Ward,A.J., Castle,J.C., Johnson,J.M., Burge,C.B. and Cooper,T.A. (2008) A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart. Proc. Natl Acad. Sci. USA, 105, 20333–20338. 28. Thomas,P.D., Kejariwal,A., Guo,N., Mi,H., Campbell,M.J., Muruganujan,A. and Lazareva-Ulitsky,B. (2006) Applications for protein sequence-function evolution data: mRNA/protein