{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,21]],"date-time":"2025-05-21T06:55:15Z","timestamp":1747810515640},"reference-count":44,"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>Extracting biological information from high-density Affymetrix arrays is a multi-step process that begins with the accurate annotation of microarray probes. Shortfalls in the original Affymetrix probe annotation have been described; however, few studies have provided rigorous solutions for routine data analysis.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Using AceView, a comprehensive human transcript database, we have reannotated the probes by matching them to RNA transcripts instead of genes. Based on this transcript-level annotation, a new probe set definition was created in which every probe in a probe set maps to a common set of AceView gene transcripts. In addition, using artificial data sets we identified that a minimal probe set size of 4 is necessary for reliable statistical summarization. We further demonstrate that applying the new probe set definition can detect specific transcript variants contributing to differential expression and it also improves cross-platform concordance.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>We conclude that our transcript-level reannotation and redefinition of probe sets complement the original Affymetrix design. Redefinitions introduce probe sets whose sizes may not support reliable statistical summarization; therefore, we advocate using our transcript-level mapping redefinition in a secondary analysis step rather than as a replacement. Knowing which specific transcripts are differentially expressed is important to properly design probe\/primer pairs for validation purposes. For convenience, we have created custom chip-description-files (CDFs) and annotation files for our new probe set definitions that are compatible with Bioconductor, Affymetrix Expression Console or third party software.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-8-108","type":"journal-article","created":{"date-parts":[[2007,5,2]],"date-time":"2007-05-02T15:24:45Z","timestamp":1178119485000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":44,"title":["Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays"],"prefix":"10.1186","volume":"8","author":[{"given":"Jun","family":"Lu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joseph C","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc L","family":"Salit","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Margaret C","family":"Cam","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,3,29]]},"reference":[{"key":"1480_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. Nat Biotechnol 1996, 14: 1675\u20131680. 10.1038\/nbt1296-1675","journal-title":"Nat Biotechnol"},{"key":"1480_CR2","doi-asserted-by":"publisher","first-page":"1359","DOI":"10.1038\/nbt1297-1359","volume":"15","author":"L Wodicka","year":"1997","unstructured":"Wodicka L, Dong H, Mittmann M, Ho MH, Lockhart DJ: Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat Biotechnol 1997, 15: 1359\u20131367. 10.1038\/nbt1297-1359","journal-title":"Nat Biotechnol"},{"key":"1480_CR3","unstructured":"Affymetrix MAS5 algorithm2006. [http:\/\/www.affymetrix.com\/support\/technical\/manual\/expression_manual.affx]"},{"key":"1480_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 WH: Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A 2001, 98: 31\u201336. 10.1073\/pnas.011404098","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1480_CR5","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1093\/biostatistics\/4.2.249","volume":"4","author":"RA Irizarry","year":"2003","unstructured":"Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4: 249\u2013264. 10.1093\/biostatistics\/4.2.249","journal-title":"Biostatistics"},{"key":"1480_CR6","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/gng015","volume":"31","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. Nucleic Acids Res 2003, 31: e15. 10.1093\/nar\/gng015","journal-title":"Nucleic Acids Res"},{"key":"1480_CR7","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1093\/bioinformatics\/bti078","volume":"21","author":"HB Nielsen","year":"2005","unstructured":"Nielsen HB, Gautier L, Knudsen S: Implementation of a gene expression index calculation method based on the PDNN model. Bioinformatics 2005, 21: 687\u2013688. 10.1093\/bioinformatics\/bti078","journal-title":"Bioinformatics"},{"key":"1480_CR8","doi-asserted-by":"publisher","first-page":"818","DOI":"10.1038\/nbt836","volume":"21","author":"L Zhang","year":"2003","unstructured":"Zhang L, Miles MF, Aldape KD: A model of molecular interactions on short oligonucleotide microarrays. Nat Biotechnol 2003, 21: 818\u2013821. 10.1038\/nbt836","journal-title":"Nat Biotechnol"},{"key":"1480_CR9","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1093\/bioinformatics\/btk046","volume":"22","author":"RA Irizarry","year":"2006","unstructured":"Irizarry RA, Wu Z, Jaffee HA: Comparison of Affymetrix GeneChip expression measures. Bioinformatics 2006, 22: 789\u2013794. 10.1093\/bioinformatics\/btk046","journal-title":"Bioinformatics"},{"key":"1480_CR10","doi-asserted-by":"publisher","first-page":"3983","DOI":"10.1093\/bioinformatics\/bti665","volume":"21","author":"L Zhou","year":"2005","unstructured":"Zhou L, Rocke DM: An expression index for Affymetrix GeneChips based on the generalized logarithm. Bioinformatics 2005, 21: 3983\u20133989. 10.1093\/bioinformatics\/bti665","journal-title":"Bioinformatics"},{"key":"1480_CR11","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1093\/bioinformatics\/btg410","volume":"20","author":"LM Cope","year":"2004","unstructured":"Cope LM, Irizarry RA, Jaffee HA, Wu Z, Speed TP: A benchmark for Affymetrix GeneChip expression measures. Bioinformatics 2004, 20: 323\u2013331. 10.1093\/bioinformatics\/btg410","journal-title":"Bioinformatics"},{"key":"1480_CR12","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1016\/j.tig.2005.12.005","volume":"22","author":"S Draghici","year":"2006","unstructured":"Draghici S, Khatri P, Eklund AC, Szallasi Z: Reliability and reproducibility issues in DNA microarray measurements. Trends Genet 2006, 22: 101\u2013109. 10.1016\/j.tig.2005.12.005","journal-title":"Trends Genet"},{"key":"1480_CR13","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":"1480_CR14","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":"1480_CR15","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":"1480_CR16","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":"1480_CR17","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1186\/1471-2105-7-276","volume":"7","author":"MJ Okoniewski","year":"2006","unstructured":"Okoniewski MJ, Miller CJ: Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. BMC Informatics 2006, 7: 276. 10.1186\/1471-2105-7-276","journal-title":"BMC Informatics"},{"key":"1480_CR18","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1186\/1471-2105-6-266","volume":"6","author":"AD Neverov","year":"2005","unstructured":"Neverov AD, Artamonova II, Nurtdinov RN, Frishman D, Gelfand M, Mironov A: Alternative splicing and protein function. BMC Bioinformatics 2005, 6: 266. 10.1186\/1471-2105-6-266","journal-title":"BMC Bioinformatics"},{"key":"1480_CR19","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1186\/1471-2105-6-183","volume":"6","author":"C Perez-Iratxeta","year":"2005","unstructured":"Perez-Iratxeta C, Andrade MA: Inconsistencies over time in 5% of NetAffx probe-to-gene annotations. BMC Bioinformatics 2005, 6: 183. 10.1186\/1471-2105-6-183","journal-title":"BMC Bioinformatics"},{"key":"1480_CR20","doi-asserted-by":"publisher","first-page":"D501","DOI":"10.1093\/nar\/gki025","volume":"33","author":"KD Pruitt","year":"2005","unstructured":"Pruitt KD, Tatusova T, Maglott DR: NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2005, 33: D501-D504. 10.1093\/nar\/gki025","journal-title":"Nucleic Acids Res"},{"key":"1480_CR21","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1016\/S0168-9525(99)01882-X","volume":"16","author":"KD Pruitt","year":"2000","unstructured":"Pruitt KD, Katz KS, Sicotte H, Maglott DR: Introducing RefSeq and LocusLink: curated human genome resources at the NCBI. Trends Genet 2000, 16: 44\u201347. 10.1016\/S0168-9525(99)01882-X","journal-title":"Trends Genet"},{"key":"1480_CR22","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":"1480_CR23","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":"1480_CR24","doi-asserted-by":"publisher","first-page":"S12","DOI":"10.1186\/gb-2006-7-s1-s12","volume":"7(Suppl 1)","author":"D Thierry-Mieg","year":"2006","unstructured":"Thierry-Mieg D, Thierry-Mieg J: The Genomewide AceView annotation closely matches the hand curated Gencode transcript annotation. Genome Biol 2006, 7(Suppl 1): S12. 10.1186\/gb-2006-7-s1-s12","journal-title":"Genome Biol"},{"key":"1480_CR25","unstructured":"Danielle and Jean Thierry-Mieg, Michel Potdevin, Mark Sienkiewicz. AceView: Identification and functional annotation of cDNA-supported genes in higher organisms2005. [http:\/\/www.ncbi.nlm.nih.gov\/IEB\/Research\/Acembly\/]"},{"key":"1480_CR26","doi-asserted-by":"publisher","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","volume":"5","author":"RC Gentleman","year":"2004","unstructured":"Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5: R80. 10.1186\/gb-2004-5-10-r80","journal-title":"Genome Biol"},{"key":"1480_CR27","doi-asserted-by":"publisher","first-page":"5676","DOI":"10.1093\/nar\/gkg763","volume":"31","author":"PK Tan","year":"2003","unstructured":"Tan PK, Downey TJ, Spitznagel EL Jr., Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC: Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 2003, 31: 5676\u20135684. 10.1093\/nar\/gkg763","journal-title":"Nucleic Acids Res"},{"key":"1480_CR28","doi-asserted-by":"crossref","unstructured":"The ENCODE (ENCyclopedia Of DNA Elements) Project Science 2004, 306: 636\u2013640. 10.1126\/science.1105136","DOI":"10.1126\/science.1105136"},{"key":"1480_CR29","unstructured":"Affymetrix spike-in data sets2005. [http:\/\/www.affymetrix.com\/support\/technical\/sample_data\/datasets.affx]"},{"key":"1480_CR30","first-page":"206","volume-title":"Molecular Modeling of Nucleic Acids","author":"EJ Forman","year":"1999","unstructured":"Forman EJ, Walton ID, Stern D, Rava RP, Trulson MO: Thermodynamics of duplex formation and mismatch discrimination on photolithogrphically synthesised oligonucleotide arrays. In Molecular Modeling of Nucleic Acids. Edited by: NB Leontis and J Santa Lucia Jr. Oxford University Press; 1999:206\u2013221."},{"key":"1480_CR31","unstructured":"Affymetrix exon arrays2006. [http:\/\/www.affymetrix.com\/support\/technical\/whitepapers\/exon_gene_signal_estimate_whitepaper.pdf]"},{"key":"1480_CR32","unstructured":"Affymetrix PLIER algorithm2006. [http:\/\/www.affymetrix.com\/support\/technical\/technotes\/plier_technote.pdf]"},{"key":"1480_CR33","unstructured":"Affymetrix exon array design technote2006. [http:\/\/www.affymetrix.com\/support\/technical\/technotes\/exon_array_design_technote.pdf]"},{"key":"1480_CR34","unstructured":"Affymetrix probe annotation2005. [http:\/\/www.affymetrix.com\/support\/technical\/byproduct.affx?cat=arrays&Human]"},{"key":"1480_CR35","unstructured":"Website for cdf files2006. [http:\/\/genomics.niddk.nih.gov\/redef.shtml]"},{"key":"1480_CR36","unstructured":"The Bioconductor Project2005. [http:\/\/www.bioconductor.org\/]"},{"key":"1480_CR37","unstructured":"NIDDK Genomics Core Lab website2006. [http:\/\/genomics.niddk.nih.gov\/links.shtml]"},{"key":"1480_CR38","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1093\/bioinformatics\/btg405","volume":"20","author":"L Gautier","year":"2004","unstructured":"Gautier L, Cope L, Bolstad BM, Irizarry RA: affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20: 307\u2013315. 10.1093\/bioinformatics\/btg405","journal-title":"Bioinformatics"},{"key":"1480_CR39","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1038\/nmeth756","volume":"2","author":"RA Irizarry","year":"2005","unstructured":"Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, Martinez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W: Multiple-laboratory comparison of microarray platforms. Nat Methods 2005, 2: 345\u2013350. 10.1038\/nmeth756","journal-title":"Nat Methods"},{"key":"1480_CR40","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1093\/nar\/gkg033","volume":"31","author":"DL Wheeler","year":"2003","unstructured":"Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, Wagner L: Database resources of the National Center for Biotechnology. Nucleic Acids Res 2003, 31: 28\u201333. 10.1093\/nar\/gkg033","journal-title":"Nucleic Acids Res"},{"key":"1480_CR41","doi-asserted-by":"publisher","first-page":"SOFTWARE0002","DOI":"10.1186\/gb-2001-2-11-software0002","volume":"2","author":"J Tsai","year":"2001","unstructured":"Tsai J, Sultana R, Lee Y, Pertea G, Karamycheva S, Antonescu V, Cho J, Parvizi B, Cheung F, Quackenbush J: RESOURCERER: a database for annotating and linking microarray resources within and across species. Genome Biol 2001, 2: SOFTWARE0002. 10.1186\/gb-2001-2-11-software0002","journal-title":"Genome Biol"},{"key":"1480_CR42","volume-title":"Statistical Applications in Genetics and Molecular Biology Vol. 3, No. 1, Article 3","author":"GK Smyth","year":"2004","unstructured":"Smyth GK: Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology Vol. 3, No. 1, Article 3. 2004."},{"key":"1480_CR43","unstructured":"The limma package website2006. [http:\/\/bioinf.wehi.edu.au\/limma\/]"},{"key":"1480_CR44","unstructured":"Human BLAT search2006. [http:\/\/genome.ucsc.edu\/cgi-bin\/hgBlat]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-108.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T01:48:38Z","timestamp":1630460918000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-8-108"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,3,29]]},"references-count":44,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["1480"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-8-108","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,3,29]]},"assertion":[{"value":"28 August 2006","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 March 2007","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 March 2007","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"108"}}