MADS+ (microarray analysis of differential splicing) is 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 a 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 exons validated out of 173 tested).
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Shihao Shen et al.
MADS+: discovery of differential splicing events from Affymetrix exon junction array data
Bioinformatics (2010) 26 (2): 268-269.