Department of Biostatistics, University of Iowa, Iowa City, IA, USA.
Bioinformatics. 2010 Jan 15;26(2):268-9. doi: 10.1093/bioinformatics/btp643. Epub 2009 Nov 17.
The Affymetrix Human Exon Junction Array is a newly designed high-density exon-sensitive microarray for global analysis of alternative splicing. Contrary to the Affymetrix exon 1.0 array, which only contains four probes per exon and no probes for exon-exon junctions, this new junction array averages eight probes per probeset targeting all exons and exon-exon junctions observed in the human mRNA/EST transcripts, representing a significant increase in the probe density for alternative splicing events. Here, we present MADS+, a computational pipeline to detect differential splicing events from the Affymetrix exon junction array data. For each alternative splicing event, MADS+ evaluates the signals of probes targeting competing transcript isoforms to identify exons or splice sites with different levels of transcript inclusion between two sample groups. MADS+ is used routinely in our analysis of Affymetrix exon junction arrays and has a high accuracy in detecting differential splicing events. For example, in a study of the novel epithelial-specific splicing regulator ESRP1, MADS+ detects hundreds of exons whose inclusion levels are dependent on ESRP1, with a RT-PCR validation rate of 88.5% (153 validated out of 173 tested).
MADS+ scripts, documentations and annotation files are available at http://www.medicine.uiowa.edu/Labs/Xing/MADSplus/.
Affymetrix 人类外显子连接点阵列是一种新设计的高密度外显子敏感微阵列，用于全面分析选择性剪接。与仅包含每个外显子四个探针且没有外显子-外显子连接点探针的 Affymetrix exon 1.0 阵列不同，这个新的连接点阵列平均每个探针组针对人类 mRNA/EST 转录本中观察到的所有外显子和外显子-外显子连接点有八个探针，这代表着对选择性剪接事件的探针密度有了显著提高。在这里，我们提出了 MADS+，这是一种从 Affymetrix 外显子连接点阵列数据中检测差异剪接事件的计算管道。对于每个选择性剪接事件，MADS+评估针对竞争转录本异构体的探针信号，以识别两个样本组之间转录本包含水平不同的外显子或剪接位点。MADS+在我们对 Affymetrix 外显子连接点阵列的分析中经常使用，并且在检测差异剪接事件方面具有很高的准确性。例如，在对新型上皮特异性剪接调节剂 ESRP1 的研究中，MADS+检测到数百个其包含水平依赖于 ESRP1 的外显子，RT-PCR 验证率为 88.5%（173 个测试中有 153 个得到验证）。
MADS+脚本、文档和注释文件可在 http://www.medicine.uiowa.edu/Labs/Xing/MADSplus/ 获得。
