{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T19:23:22Z","timestamp":1773084202444,"version":"3.50.1"},"reference-count":16,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2007,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Improvements in genome sequence annotation revealed discrepancies in the original probeset\/gene assignment in Affymetrix microarray and the existence of differences between annotations and effective alignments of probes and transcription products. In the current generation of Affymetrix human GeneChips, most probesets include probes matching transcripts from more than one gene and probes which do not match any transcribed sequence.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We developed a novel set of custom Chip Definition Files (CDF) and the corresponding Bioconductor libraries for Affymetrix human GeneChips, based on the information contained in the GeneAnnot database. GeneAnnot-based CDFs are composed of unique custom-probesets, including only probes matching a single gene.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>GeneAnnot-based custom CDFs solve the problem of a reliable reconstruction of expression levels and eliminate the existence of more than one probeset per gene, which often leads to discordant expression signals for the same transcript when gene differential expression is the focus of the analysis. GeneAnnot CDFs are freely distributed and fully compliant with Affymetrix standards and all available software for gene expression analysis. The CDF libraries are available from <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.xlab.unimo.it\/GA_CDF\" ext-link-type=\"uri\">http:\/\/www.xlab.unimo.it\/GA_CDF<\/jats:ext-link>, along with supplementary information (CDF libraries, installation guidelines and R code, CDF statistics, and analysis results).<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-8-446","type":"journal-article","created":{"date-parts":[[2007,11,15]],"date-time":"2007-11-15T19:14:11Z","timestamp":1195154051000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":81,"title":["Novel definition files for human GeneChips based on GeneAnnot"],"prefix":"10.1186","volume":"8","author":[{"given":"Francesco","family":"Ferrari","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefania","family":"Bortoluzzi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessandro","family":"Coppe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexandra","family":"Sirota","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marilyn","family":"Safran","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Shmoish","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sergio","family":"Ferrari","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Doron","family":"Lancet","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gian Antonio","family":"Danieli","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Silvio","family":"Bicciato","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,11,15]]},"reference":[{"key":"1818_CR1","doi-asserted-by":"publisher","first-page":"e74","DOI":"10.1093\/nar\/gnh071","volume":"32","author":"BH Mecham","year":"2004","unstructured":"Mecham BH, Klus GT, Strovel J, Augustus M, Byrne D, Bozso P, Wetmore DZ, Mariani TJ, Kohane IS, Szallasi Z: Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res 2004, 32: e74. 10.1093\/nar\/gnh071","journal-title":"Nucleic Acids Res"},{"key":"1818_CR2","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1186\/1471-2105-5-111","volume":"5","author":"L Gautier","year":"2004","unstructured":"Gautier L, Moller M, Friis-Hansen L, Knudsen S: Alternative mapping of probes to genes for Affymetrix chips. BMC Bioinformatics 2004, 5: 111. 10.1186\/1471-2105-5-111","journal-title":"BMC Bioinformatics"},{"key":"1818_CR3","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1016\/j.ygeno.2004.11.004","volume":"85","author":"J Zhang","year":"2005","unstructured":"Zhang J, Finney RP, Clifford RJ, Derr LK, Buetow KH: Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach. Genomics 2005, 85: 297\u2013308. 10.1016\/j.ygeno.2004.11.004","journal-title":"Genomics"},{"key":"1818_CR4","doi-asserted-by":"publisher","first-page":"e31","DOI":"10.1093\/nar\/gni027","volume":"33","author":"J Harbig","year":"2005","unstructured":"Harbig J, Sprinkle R, Enkemann SA: A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array. Nucleic Acids Res 2005, 33: e31. 10.1093\/nar\/gni027","journal-title":"Nucleic Acids Res"},{"key":"1818_CR5","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1186\/1471-2105-6-107","volume":"6","author":"SL Carter","year":"2005","unstructured":"Carter SL, Eklund AC, Mecham BH, Kohane IS, Szallasi Z: Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics 2005, 6: 107. 10.1186\/1471-2105-6-107","journal-title":"BMC Bioinformatics"},{"key":"1818_CR6","doi-asserted-by":"publisher","first-page":"e175","DOI":"10.1093\/nar\/gni179","volume":"33","author":"M Dai","year":"2005","unstructured":"Dai M, Wang P, Boyd AD, Kostov G, Athey B, Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, Watson SJ, Meng F: Evolving gene\/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 2005, 33: e175. 10.1093\/nar\/gni179","journal-title":"Nucleic Acids Res"},{"key":"1818_CR7","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1186\/1471-2105-8-108","volume":"8","author":"J Lu","year":"2007","unstructured":"Lu J, Lee JC, Salit ML, Cam MC: Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: high-resolution annotation for microarrays. BMC Bioinformatics 2007, 8: 108. 10.1186\/1471-2105-8-108","journal-title":"BMC Bioinformatics"},{"key":"1818_CR8","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/1471-2105-8-13","volume":"8","author":"MA Stalteri","year":"2007","unstructured":"Stalteri MA, Harrison AP: Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. BMC Bioinformatics 2007, 8: 13. 10.1186\/1471-2105-8-13","journal-title":"BMC Bioinformatics"},{"key":"1818_CR9","unstructured":"Dai custom CDF[http:\/\/brainarray.mbni.med.umich.edu\/Brainarray\/]"},{"key":"1818_CR10","doi-asserted-by":"publisher","first-page":"1457","DOI":"10.1093\/bioinformatics\/bth081","volume":"20","author":"V Chalifa-Caspi","year":"2004","unstructured":"Chalifa-Caspi V, Yanai I, Ophir R, Rosen N, Shmoish M, Benjamin-Rodrig H, Shklar M, Stein TI, Shmueli O, Safran M, Lancet D: GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes. 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Bioessays 2006, 28: 739\u2013746. 10.1002\/bies.20433","journal-title":"Bioessays"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-446.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T10:16:10Z","timestamp":1630491370000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-8-446"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,11,15]]},"references-count":16,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["1818"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-8-446","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,11,15]]},"assertion":[{"value":"25 June 2007","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 November 2007","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 November 2007","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"446"}}