Gene Array Analyzer (GAA): Alternative usage of gene arrays to study alternative splicing events (MoGene array)

The latest version of microarrays released by Affymetrix, the GeneChip Gene 1.0 ST Arrays (gene arrays), are designed in a similar fashion as exon arrays, which enables to identify differentially expressed exons, rather than only the expression level of whole transcripts. Here, we propose an extension, Gene Array Analyzer (GAA), to our previously published Exon Array Analyzer (EAA). GAA enables to analyse gene arrays on exon level and therefore supports to identify alternative splicing with gene arrays. To show the applicability of GAA, we used gene arrays to profile alternative splice events during the development of the heart. Further re-analysis of published gene arrays could show, that some of these splice events reoccur under pathological conditions. The web interface of GAA is user friendly, functional without set up and freely available at http://GAA.mpi-bn.mpg.de. Alternative splicing and gene expression analysis during development of the heart and cardiomyocyte differentiation.Affymetrix公司发布的最新一代微阵列（microarrays）产品GeneChip Gene 1.0 ST Arrays（基因芯片），其设计思路与外显子芯片（exon arrays）相仿，不仅可检测完整转录本的表达水平，还能识别差异表达的外显子。在此基础上，我们对此前发表的外显子芯片分析工具（Exon Array Analyzer, EAA）进行拓展，推出基因芯片分析工具（Gene Array Analyzer, GAA）。GAA可在外显子层面开展基因芯片数据分析，进而支持利用基因芯片识别可变剪接事件。为验证GAA的适用性，我们利用该基因芯片对心脏发育过程中的可变剪接事件进行了表达谱分析。进一步对已发表的基因芯片数据进行重新分析后发现，部分此类剪接事件在病理状态下也会重现。GAA的网页界面操作便捷友好，无需额外配置即可使用，且可通过http://GAA.mpi-bn.mpg.de免费获取。本数据集涵盖心脏发育及心肌细胞分化过程中的可变剪接与基因表达分析相关数据。