{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T01:11:52Z","timestamp":1773277912762,"version":"3.50.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2889,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Microarray designs have become increasingly probe-rich, enabling targeting of specific features, such as individual exons or single nucleotide polymorphisms. These arrays have the potential to achieve quantitative high-throughput estimates of transcript abundances, but currently these estimates are affected by biases due to cross-hybridization, in which probes hybridize to off-target transcripts.<\/jats:p>\n               <jats:p>Results: To study cross-hybridization, we map Affymetrix exon array probes to a set of annotated mRNA transcripts, allowing a small number of mismatches or insertion\/deletions between the two sequences. Based on a systematic study of the degree to which probes with a given match type to a transcript are affected by cross-hybridization, we developed a strategy to correct for cross-hybridization biases of gene-level expression estimates. Comparison with Solexa ultra high-throughput sequencing data demonstrates that correction for cross-hybridization leads to a significant improve-ment of gene expression estimates.<\/jats:p>\n               <jats:p>Availability: We provide mappings between human and mouse exon array probes and off-target transcripts and provide software extending the GeneBASE program for generating gene-level expression estimates including the cross-hybridization correction http:\/\/biogibbs.stanford.edu\/~kkapur\/GeneBase\/.<\/jats:p>\n               <jats:p>Contact: \u00a0whwong@stanford.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn571","type":"journal-article","created":{"date-parts":[[2008,11,5]],"date-time":"2008-11-05T02:02:34Z","timestamp":1225850554000},"page":"2887-2893","source":"Crossref","is-referenced-by-count":31,"title":["Cross-hybridization modeling on Affymetrix exon arrays"],"prefix":"10.1093","volume":"24","author":[{"given":"Karen","family":"Kapur","sequence":"first","affiliation":[{"name":"1 Department of Statistics, 2Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, 3Department of Internal Medicine and Department of Biomedical Engineering, University of Iowa, Iowa City, IA and 4Department of Health Research and Policy, Stanford University, Stanford, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hui","family":"Jiang","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, 2Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, 3Department of Internal Medicine and Department of Biomedical Engineering, University of Iowa, Iowa City, IA and 4Department of Health Research and Policy, Stanford University, Stanford, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Xing","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, 2Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, 3Department of Internal Medicine and Department of Biomedical Engineering, University of Iowa, Iowa City, IA and 4Department of Health Research and Policy, Stanford University, Stanford, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wing Hung","family":"Wong","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, 2Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, 3Department of Internal Medicine and Department of Biomedical Engineering, University of Iowa, Iowa City, IA and 4Department of Health Research and Policy, Stanford University, Stanford, CA, USA"},{"name":"1 Department of Statistics, 2Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, 3Department of Internal Medicine and Department of Biomedical Engineering, University of Iowa, Iowa City, IA and 4Department of Health Research and Policy, Stanford University, Stanford, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,11,4]]},"reference":[{"key":"2023020212300472000_B1","volume-title":"Affymetrix technical documentation for exon array probe annotations.","author":"Affymetrix","year":"2005"},{"key":"2023020212300472000_B2","volume-title":"Exon array design datasheet.","author":"Affymetrix","year":"2005"},{"key":"2023020212300472000_B3","doi-asserted-by":"crossref","first-page":"1636","DOI":"10.1101\/gad.1558107","article-title":"A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons","volume":"21","author":"Boutz","year":"2007","journal-title":"Genes Dev."},{"key":"2023020212300472000_B4","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1186\/1471-2105-8-461","article-title":"In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation","volume":"8","author":"Casneuf","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023020212300472000_B5","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":"2023020212300472000_B6","doi-asserted-by":"crossref","first-page":"1071","DOI":"10.1038\/nbt0906-1071","article-title":"Replacing cRNA targets with cdna reduces microarray cross-hybridization","volume":"24","author":"Eklund","year":"2006","journal-title":"Nat. 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