{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,11]],"date-time":"2025-04-11T08:29:21Z","timestamp":1744360161992},"reference-count":8,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>DNA microarray probes are designed to match particular mRNA transcripts, often based on expressed sequences like ESTs, or cDNAs, many times incomplete. As a result, the relations between probes and genes can change as the sequence data are updated. However, it is frequent that the reported results of microarray analyses are given just as lists of genes without any reference to the underlying probes.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We show for a particular commercial microarray design that the number of probes associated to some genes change with time. These changes concern approximately 5% of the probe sets across the history of annotation releases over a two year span.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>We recommend to report probe set identifiers when publishing microarray results, and to submit those analyses to microarray public databases to ensure that the interpretation of the data is updated with the latest set of annotations.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/1471-2105-6-183","type":"journal-article","created":{"date-parts":[[2005,7,23]],"date-time":"2005-07-23T18:13:32Z","timestamp":1122142412000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Inconsistencies over time in 5% of NetAffx probe-to-gene annotations"],"prefix":"10.1186","volume":"6","author":[{"given":"Carolina","family":"Perez-Iratxeta","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Miguel A","family":"Andrade","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2005,7,20]]},"reference":[{"key":"508_CR1","doi-asserted-by":"publisher","first-page":"1795","DOI":"10.1016\/j.febslet.2005.02.020","volume":"579","author":"C Perez-Iratxeta","year":"2005","unstructured":"Perez-Iratxeta C, Palidwor G, Porter CG, Sanche NA, Huska MR, Suomela BP, Muro EM, Krzyzanowski P, Hughes E, Campbell PA, Rudnicki MA, Andrade MA: Study of stem cell function using microarray experiments. FEBS Letters 2005, 579: 1795\u20131801. 10.1016\/j.febslet.2005.02.020","journal-title":"FEBS Letters"},{"key":"508_CR2","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1093\/nar\/gkg121","volume":"31","author":"G Liu","year":"2003","unstructured":"Liu G, Loraine AE, Shigeta R, Cline M, Cheng J, Valmeekam V, Sun S, Kulp D, Siani-Rose MA: NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res 2003, 31: 82\u201386. 10.1093\/nar\/gkg121","journal-title":"Nucleic Acids Res"},{"issue":"Database Issue","key":"508_CR3","doi-asserted-by":"publisher","first-page":"D39","DOI":"10.1093\/nar\/gki062","volume":"33","author":"DL Wheeler","year":"2005","unstructured":"Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Church DM, DiCuccio M, Edgar R, Federhen S, Helmberg W, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pontius JU, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2005, 33(Database Issue):D39\u201345. 10.1093\/nar\/gki062","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"508_CR4","doi-asserted-by":"publisher","first-page":"D35","DOI":"10.1093\/nar\/gkh073","volume":"32","author":"DL Wheeler","year":"2004","unstructured":"Wheeler DL, Church DM, Edgar R, Federhen S, Helmberg W, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Suzek TO, Tatusova TA, Wagner L: Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res 2004, 32(Database issue):D35\u201340. 10.1093\/nar\/gkh073","journal-title":"Nucleic Acids Res"},{"key":"508_CR5","doi-asserted-by":"publisher","first-page":"3522","DOI":"10.1099\/mic.0.27637-0","volume":"150","author":"C Ball","year":"2004","unstructured":"Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Icahn C, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N: An open letter on microarray data from the MGED Society. Microbiology 2004, 150: 3522\u20133524. 10.1099\/mic.0.27637-0","journal-title":"Microbiology"},{"key":"508_CR6","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":"508_CR7","doi-asserted-by":"publisher","first-page":"W471","DOI":"10.1093\/nar\/gkh452","volume":"32","author":"FM Roche","year":"2004","unstructured":"Roche FM, Hokamp K, Acab M, Babiuk LA, Hancock RE, Brinkman FS: ProbeLynx: a tool for updating the association of microarray probes to genes. Nucleic Acids Res 2004, 32: W471\u20134. 10.1093\/nar\/gkh123","journal-title":"Nucleic Acids Res"},{"key":"508_CR8","volume-title":"Bioinformatics","author":"HS Leong","year":"2005","unstructured":"Leong HS, Yates T, Wilson C, Miller CJ: ADAPT: A Database of Affymetrix Probesets and Transcripts. Bioinformatics 2005."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-183.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T17:56:18Z","timestamp":1706810178000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-183"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,7,20]]},"references-count":8,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2005,12]]}},"alternative-id":["508"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-183","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,7,20]]},"assertion":[{"value":"30 March 2005","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 July 2005","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 July 2005","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"183"}}