{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T08:56:43Z","timestamp":1762160203920,"version":"build-2065373602"},"reference-count":18,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2004,8,14]],"date-time":"2004-08-14T00:00:00Z","timestamp":1092441600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"},{"start":{"date-parts":[[2004,8,14]],"date-time":"2004-08-14T00:00:00Z","timestamp":1092441600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"Abstract<\/jats:title>\n Background<\/jats:title>\n Short oligonucleotide arrays have several probes measuring the expression level of each target transcript. Therefore the selection of probes is a key component for the quality of measurements. However, once probes have been selected and synthesized on an array, it is still possible to re-evaluate the results using an updated mapping of probes to genes, taking into account the latest biological knowledge available.<\/jats:p>\n <\/jats:sec>\n Methods<\/jats:title>\n We investigated how probes found on recent commercial microarrays for human genes (Affymetrix HG-U133A) were matching a recent curated collection of human transcripts: the NCBI RefSeq database. We also built mappings and used them in place of the original probe to genes associations provided by the manufacturer of the arrays.<\/jats:p>\n <\/jats:sec>\n Results<\/jats:title>\n In a large number of cases, 36%, the probes matching a reference sequence were consistent with the grouping of probes by the manufacturer of the chips. For the remaining cases there were discrepancies and we show how that can affect the analysis of data.<\/jats:p>\n <\/jats:sec>\n Conclusions<\/jats:title>\n While the probes on Affymetrix arrays remain the same for several years, the biological knowledge concerning the genomic sequences evolves rapidly. Using up-to-date knowledge can apparently change the outcome of an analysis.<\/jats:p>\n <\/jats:sec>","DOI":"10.1186\/1471-2105-5-111","type":"journal-article","created":{"date-parts":[[2004,8,18]],"date-time":"2004-08-18T06:23:03Z","timestamp":1092810183000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":92,"title":["Alternative mapping of probes to genes for Affymetrix chips"],"prefix":"10.1186","volume":"5","author":[{"given":"Laurent","family":"Gautier","sequence":"first","affiliation":[]},{"given":"Morten","family":"M\u00f8ller","sequence":"additional","affiliation":[]},{"given":"Lennart","family":"Friis-Hansen","sequence":"additional","affiliation":[]},{"given":"Steen","family":"Knudsen","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2004,8,14]]},"reference":[{"key":"227_CR1","doi-asserted-by":"publisher","first-page":"1675","DOI":"10.1038\/nbt1296-1675","volume":"14","author":"DJ Lockhart","year":"1996","unstructured":"Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL: Expression Monitoring by hybridization to high-density oligonucleotide arrays.\n Nature Biotechnology 1996, 14: 1675\u20131680. 10.1038\/nbt1296-1675","journal-title":"Nature Biotechnology"},{"key":"227_CR2","volume-title":"version 4, Affymetrix, Santa Clara, CA","author":"Affymetrix","year":"1999","unstructured":"Affymetrix: Affymetrix Microarray Suite User Guide.\n version 4, Affymetrix, Santa Clara, CA 1999."},{"key":"227_CR3","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1016\/S0025-5564(01)00100-6","volume":"176","author":"E Lazaridis","year":"2002","unstructured":"Lazaridis E, Sinibaldi D, Bloom G, Mane S, Jove R: A simple method to improve probe set estimates from oligonucleotides arrays.\n Mathematical Biosciences 2002, 176: 53\u201358. 10.1016\/S0025-5564(01)00100-6","journal-title":"Mathematical Biosciences"},{"key":"227_CR4","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1073\/pnas.98.1.31","volume":"98","author":"C Li","year":"2001","unstructured":"Li C, Wong W: Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection.\n Proceedings of the National Academy of Science U S A 2001, 98: 31\u201336. 10.1073\/pnas.011404098","journal-title":"Proceedings of the National Academy of Science U S A"},{"key":"227_CR5","volume-title":"Nucleic Acids Research","author":"RA Irizarry","year":"2003","unstructured":"Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP: Summaries of Affymetrix GeneChip probe level data.\n Nucleic Acids Research 2003., 31:"},{"key":"227_CR6","volume-title":"version 5, Affymetrix, Santa Clara, CA","author":"Affymetrix","year":"2002","unstructured":"Affymetrix: Affymetrix Microarray Suite User Guide.\n version 5, Affymetrix, Santa Clara, CA 2002."},{"key":"227_CR7","first-page":"827","volume":"405","author":"Z Li","year":"2003","unstructured":"Li Z, F MM, D AK: A model of molecular interactions on short oligonucleotide microarrays.\n Nature Biotechnology 2003, 405: 827\u2013836.","journal-title":"Nature Biotechnology"},{"key":"227_CR8","volume-title":"software package","author":"W Zhijin","year":"2003","unstructured":"Zhijin W: gcrma.\n software package 2003. [Http:\/\/www.bioconductor.org\/repository\/release1.4\/package\/html\/gcrma.html]"},{"key":"227_CR9","volume-title":"Journal of Climate","author":"V Ventura","year":"2004","unstructured":"Ventura V, Paciorek C, Risbey J: Controlling the proportion of falsely-rejected hypotheses when conducting multiple tests with climatological data.\n Journal of Climate 2004."},{"key":"227_CR10","volume-title":"Tech Rep 755, Carnegie Mellon University, Statistics department","author":"V Ventura","year":"2004","unstructured":"Ventura V, Paciorek C, Risbey J: Controlling the proportion of falsely-rejected hypotheses when conducting multiple tests with climatological data.\n Tech Rep 755, Carnegie Mellon University, Statistics department 2004."},{"key":"227_CR11","doi-asserted-by":"crossref","unstructured":"Antipova AA, Tamayo P, Golub TR: A strategy for oligonucleotide microarray probe reduction.\n Genome Biol 2002., 3(12):","DOI":"10.1186\/gb-2002-3-12-research0073"},{"key":"227_CR12","volume-title":"Nucleic Acids Res","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.\n Nucleic Acids Res 2003., 31:"},{"key":"227_CR13","unstructured":"[http:\/\/www.ncbi.nlm.nih.gov\/RefSeq\/]"},{"key":"227_CR14","unstructured":"Company TA[http:\/\/www.affymetrix.com]"},{"key":"227_CR15","unstructured":"Team BD: The Bioconductor Project.[http:\/\/www.bioconductor.org]"},{"key":"227_CR16","first-page":"1","volume":"1","author":"F Naef","year":"2001","unstructured":"Naef F, Lim DA, Patil N, Magnasco MO: From features to expression: High density oligonucleotide array analysis revisited.\n Tech Report 2001, 1: 1\u20139.","journal-title":"Tech Report"},{"key":"227_CR17","volume-title":"Bioinformatics","author":"L Gautier","year":"2003","unstructured":"Gautier L, Cope L, Bolstad BM, Irizarry RA: affy \u2013 Analysis of Affymetrix GeneChip data at the probe level.\n Bioinformatics 2003."},{"issue":"Suppl 1","key":"227_CR18","doi-asserted-by":"publisher","first-page":"S96","DOI":"10.1093\/bioinformatics\/18.suppl_1.S96","volume":"18","author":"W Huber","year":"2002","unstructured":"Huber W, von Heydebreck A, Sueltmann H, Poutska A, Vingron M: Variance stabilization applied to microarray data calibration and to the quantification of differential expression.\n Bioinformatics 2002, 18(Suppl 1):S96-S104.","journal-title":"Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-5-111.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/1471-2105-5-111\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-5-111.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T12:16:34Z","timestamp":1728303394000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-5-111"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,8,14]]},"references-count":18,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2004,12]]}},"alternative-id":["227"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-5-111","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2004,8,14]]},"assertion":[{"value":"16 March 2004","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 August 2004","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 August 2004","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"111"}}