{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T23:51:46Z","timestamp":1773273106130,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Splice junction microarrays and RNA-seq are two popular ways of quantifying splice variants within a cell. Unfortunately, isoform expressions cannot always be determined from the expressions of individual exons and splice junctions. While this issue has been noted before, the extent of the problem on various platforms has not yet been explored, nor have potential remedies been presented.<\/jats:p>\n               <jats:p>Results: We propose criteria that will guarantee identifiability of an isoform deconvolution model on exon and splice junction arrays and in RNA-Seq. We show that up to 97% of 2256 alternatively spliced human genes selected from the RefSeq database lead to identifiable gene models in RNA-seq, with similar results in mouse. However, in the Human Exon array only 26% of these genes lead to identifiable models, and even in the most comprehensive splice junction array only 69% lead to identifiable models.<\/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\/btp544","type":"journal-article","created":{"date-parts":[[2009,9,18]],"date-time":"2009-09-18T03:59:51Z","timestamp":1253246391000},"page":"3056-3059","source":"Crossref","is-referenced-by-count":53,"title":["Identifiability of isoform deconvolution from junction arrays and RNA-Seq"],"prefix":"10.1093","volume":"25","author":[{"given":"David","family":"Hiller","sequence":"first","affiliation":[{"name":"1 Department of Statistics, 2 Institute for Computational and Mathematical Engineering, 3 Stanford Genome Technology Center and 4 Department of Health Research and Policy, Stanford University, Stanford, CA 94305, USA"}]},{"given":"Hui","family":"Jiang","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, 2 Institute for Computational and Mathematical Engineering, 3 Stanford Genome Technology Center and 4 Department of Health Research and Policy, Stanford University, Stanford, CA 94305, USA"},{"name":"1 Department of Statistics, 2 Institute for Computational and Mathematical Engineering, 3 Stanford Genome Technology Center and 4 Department of Health Research and Policy, Stanford University, Stanford, CA 94305, USA"}]},{"given":"Weihong","family":"Xu","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, 2 Institute for Computational and Mathematical Engineering, 3 Stanford Genome Technology Center and 4 Department of Health Research and Policy, Stanford University, Stanford, CA 94305, USA"}]},{"given":"Wing Hung","family":"Wong","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, 2 Institute for Computational and Mathematical Engineering, 3 Stanford Genome Technology Center and 4 Department of Health Research and Policy, Stanford University, Stanford, CA 94305, USA"},{"name":"1 Department of Statistics, 2 Institute for Computational and Mathematical Engineering, 3 Stanford Genome Technology Center and 4 Department of Health Research and Policy, Stanford University, Stanford, CA 94305, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,9,16]]},"reference":[{"key":"2023013112155762200_B1","doi-asserted-by":"crossref","first-page":"R46","DOI":"10.1186\/gb-2008-9-2-r46","article-title":"Space: an algorithm to predict and quantify alternatively spliced isoforms using microarrays","volume":"9","author":"Anton","year":"2008","journal-title":"Genome Biol."},{"key":"2023013112155762200_B2","doi-asserted-by":"crossref","first-page":"D610","DOI":"10.1093\/nar\/gkl996","article-title":"Ensembl 2007","volume":"35","author":"Hubbard","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023013112155762200_B3","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1093\/bioinformatics\/btp113","article-title":"Statistical inferences for isoform expression in RNA-seq","volume":"25","author":"Jiang","year":"2009","journal-title":"Bioinformatics"},{"key":"2023013112155762200_B4","doi-asserted-by":"crossref","first-page":"D493","DOI":"10.1093\/nar\/gkh103","article-title":"The UCSC Table Browser data retrieval tool","volume":"32","author":"Karolchik","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023013112155762200_B5","doi-asserted-by":"crossref","first-page":"e180","DOI":"10.1093\/nar\/gnh173","article-title":"Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data","volume":"32","author":"Le","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023013112155762200_B6","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. 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