{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T13:48:51Z","timestamp":1778593731034,"version":"3.51.4"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: 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\u2013exon junctions, this new junction array averages eight probes per probeset targeting all exons and exon\u2013exon 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).<\/jats:p>\n               <jats:p>Availability: MADS+ scripts, documentations and annotation files are available at http:\/\/www.medicine.uiowa.edu\/Labs\/Xing\/MADSplus\/.<\/jats:p>\n               <jats:p>Contact: \u00a0yi-xing@uiowa.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp643","type":"journal-article","created":{"date-parts":[[2009,11,19]],"date-time":"2009-11-19T01:13:16Z","timestamp":1258593196000},"page":"268-269","source":"Crossref","is-referenced-by-count":32,"title":["MADS+: discovery of differential splicing events from Affymetrix exon junction array data"],"prefix":"10.1093","volume":"26","author":[{"given":"Shihao","family":"Shen","sequence":"first","affiliation":[{"name":"1 Department of Biostatistics, University of Iowa, Iowa City, IA, 2 Cell and Molecular Biology Graduate Group, 3 Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, 4 Department of Internal Medicine and 5 Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claude C.","family":"Warzecha","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, University of Iowa, Iowa City, IA, 2 Cell and Molecular Biology Graduate Group, 3 Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, 4 Department of Internal Medicine and 5 Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Russ P.","family":"Carstens","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, University of Iowa, Iowa City, IA, 2 Cell and Molecular Biology Graduate Group, 3 Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, 4 Department of Internal Medicine and 5 Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA"},{"name":"1 Department of Biostatistics, University of Iowa, Iowa City, IA, 2 Cell and Molecular Biology Graduate Group, 3 Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, 4 Department of Internal Medicine and 5 Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Xing","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, University of Iowa, Iowa City, IA, 2 Cell and Molecular Biology Graduate Group, 3 Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, 4 Department of Internal Medicine and 5 Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA"},{"name":"1 Department of Biostatistics, University of Iowa, Iowa City, IA, 2 Cell and Molecular Biology Graduate Group, 3 Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, 4 Department of Internal Medicine and 5 Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA"},{"name":"1 Department of Biostatistics, University of Iowa, Iowa City, IA, 2 Cell and Molecular Biology Graduate Group, 3 Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, 4 Department of Internal Medicine and 5 Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,11,17]]},"reference":[{"key":"2023012508213359000_B1","doi-asserted-by":"crossref","first-page":"1379","DOI":"10.1101\/gad.1788009","article-title":"Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes","volume":"23","author":"Blencowe","year":"2009","journal-title":"Genes Dev."},{"key":"2023012508213359000_B2","doi-asserted-by":"crossref","first-page":"R64","DOI":"10.1186\/gb-2007-8-4-r64","article-title":"Discovery of tissue-specific exons using comprehensive human exon microarrays","volume":"8","author":"Clark","year":"2007","journal-title":"Genome Biol."},{"key":"2023012508213359000_B3","doi-asserted-by":"crossref","first-page":"R82","DOI":"10.1186\/gb-2007-8-5-r82","article-title":"Exon arrays provide accurate assessments of gene expression","volume":"8","author":"Kapur","year":"2007","journal-title":"Genome Biol."},{"key":"2023012508213359000_B4","doi-asserted-by":"crossref","first-page":"R77","DOI":"10.1186\/gb-2009-10-7-r77","article-title":"Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies","volume":"10","author":"Laajala","year":"2009","journal-title":"Genome Biol."},{"key":"2023012508213359000_B5","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1073\/pnas.98.1.31","article-title":"Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection","volume":"98","author":"Li","year":"2001","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012508213359000_B6","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1016\/j.molcel.2009.01.025","article-title":"ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing","volume":"33","author":"Warzecha","year":"2009","journal-title":"Mol. Cell"},{"key":"2023012508213359000_B7","doi-asserted-by":"crossref","first-page":"e88","DOI":"10.1371\/journal.pone.0000088","article-title":"Probe selection and expression index computation of affymetrix exon arrays","volume":"1","author":"Xing","year":"2006","journal-title":"PLoS ONE"},{"key":"2023012508213359000_B8","doi-asserted-by":"crossref","first-page":"1470","DOI":"10.1261\/rna.1070208","article-title":"MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays","volume":"14","author":"Xing","year":"2008","journal-title":"RNA"},{"key":"2023012508213359000_B9","doi-asserted-by":"crossref","first-page":"3363","DOI":"10.1182\/blood-2008-05-160325","article-title":"Alternative pre-mRNA splicing switches modulate gene expression in late erythropoiesis","volume":"113","author":"Yamamoto","year":"2009","journal-title":"Blood"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/2\/268\/48857143\/bioinformatics_26_2_268.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/2\/268\/48857143\/bioinformatics_26_2_268.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:22:07Z","timestamp":1674634927000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/2\/268\/209989"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,11,17]]},"references-count":9,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2010,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp643","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,1,15]]},"published":{"date-parts":[[2009,11,17]]}}}