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MADS+ - discovery of differential splicing events from Affymetrix exon junction array data (RRID:SCR_007189)Copy Citation Copied
URL: http://www.mimg.ucla.edu/faculty/xing/MADSplus/instructions.html
Proper Citation: MADS+ - discovery of differential splicing events from Affymetrix exon junction array data (RRID:SCR_007189)
Description: 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 4 probes per exon and no probes for exon-exon junctions, this new junction array averages 8 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 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).
Abbreviations: MADS+
Resource Type: service resource, source code, software resource
Keywords: algorithm
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