title: MADS+: discovery of differential splicing events from Affymetrix exon junction array data.
abstract: BACKGROUND
  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).
  
  
  BACKGROUND
  MADS+ scripts, documentations and annotation files are available at http://www.medicine.uiowa.edu/Labs/Xing/MADSplus/.
authors.affiliation: Department of Biostatistics, University of Iowa, Iowa City, IA, USA.
authors.forename: Shihao
authors.initials: S
authors.lastname: Shen
authors.forename: Claude C
authors.initials: CC
authors.lastname: Warzecha
authors.forename: Russ P
authors.initials: RP
authors.lastname: Carstens
authors.forename: Yi
authors.initials: Y
authors.lastname: Xing
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D005091:Exons; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software