Abstract
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+ sc...Continue Reading
References
Jan 3, 2001·Proceedings of the National Academy of Sciences of the United States of America·C Li, W H Wong
Dec 22, 2006·PloS One·Yi XingWing Hung Wong
Apr 26, 2007·Genome Biology·Tyson A ClarkJohn E Blume
May 17, 2007·Genome Biology·Karen KapurWing Hung Wong
Jun 21, 2008·RNA·Yi XingWing Hung Wong
Feb 7, 2009·Blood·Miki L YamamotoJohn G Conboy
Mar 17, 2009·Molecular Cell·Claude C WarzechaRuss P Carstens
Jun 17, 2009·Genes & Development·Benjamin J BlencoweLeo J Lee
Jul 18, 2009·Genome Biology·Essi LaajalaLaura L Elo
Citations
May 13, 2010·Human Molecular Genetics·Lan LinYi Xing
Sep 25, 2010·Nucleic Acids Research·Song LiuYi Xing
Jul 13, 2011·Nucleic Acids Research·Ping ChenSampsa Hautaniemi
Feb 9, 2013·Nucleic Acids Research·Manli ShenStefan Stamm
Feb 23, 2012·Molecular and Cellular Biology·Kimberly A DittmarRussell P Carstens
Mar 30, 2012·RNA·Erik S AndersonDouglas L Black
Jul 12, 2013·PloS One·Nan DengDongxiao Zhu
Nov 20, 2013·PloS One·Laurie A HeinickeRuss P Carstens
Dec 21, 2013·PloS One·Zhaiyi ZhangStefan Stamm
Mar 14, 2014·Nucleic Acids Research·Paolo ConvertiniStefan Stamm
May 21, 2014·ELife·Magdalena M MaslonJavier F Cáceres
May 15, 2013·Statistics in Biosciences·Wei Sun, Yijuan Hu
Mar 6, 2016·Briefings in Bioinformatics·Matthew DapasRamana V Davuluri
Jul 7, 2015·Scientific Reports·Junhee SeokWenzhong Xiao
Aug 17, 2010·The EMBO Journal·Claude C WarzechaRuss P Carstens
Jul 30, 2015·Gene·Marina FalaleevaStefan Stamm
Apr 3, 2013·Biochimica Et Biophysica Acta·Paolo ConvertiniStefan Stamm
Nov 13, 2010·Trends in Cell Biology·Frank Gertler, John Condeelis
May 28, 2013·Cell Metabolism·Ivan BabicPaul S Mischel
Aug 29, 2014·PloS One·Bin WuLianfeng Gu
Jun 19, 2016·BMC Genomics·Juan P RomeroAngel Rubio
Jun 12, 2018·Molecular Neuropsychiatry·Marquis Philip VawterTerry W Osborn
Feb 2, 2018·Briefings in Bioinformatics·Fernando CarazoAngel Rubio
Sep 27, 2018·BMC Genomics·Juan P RomeroAngel Rubio
Dec 29, 2013·Cancer Research·Fernando J de MiguelRuben Pio