{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,4,22]],"date-time":"2023-04-22T05:39:00Z","timestamp":1682141940111},"reference-count":39,"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":[[2009,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>The MAQC project demonstrated that microarrays with comparable content show inter- and intra-platform reproducibility. However, since the content of gene databases still increases, the development of new generations of microarrays covering new content is mandatory. To better understand the potential challenges updated microarray content might pose on clinical and biological projects we developed a methodology consisting of <jats:italic>in silico<\/jats:italic> analyses combined with performance analysis using real biological samples.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Here we clearly demonstrate that not only oligonucleotide design but also database content and annotation strongly influence comparability and performance of subsequent generations of microarrays. Additionally, using human blood samples and purified T lymphocyte subsets as two independent examples, we show that a performance analysis using biological samples is crucial for the assessment of consistency and differences.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>This study provides an important resource assisting investigators in comparing microarrays of updated content especially when working in a clinical or regulatory setting.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-10-186","type":"journal-article","created":{"date-parts":[[2009,7,15]],"date-time":"2009-07-15T18:14:03Z","timestamp":1247681643000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays"],"prefix":"10.1186","volume":"10","author":[{"given":"Daniela","family":"Eggle","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Svenja","family":"Debey-Pascher","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc","family":"Beyer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joachim L","family":"Schultze","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,6,18]]},"reference":[{"issue":"2","key":"2916_CR1","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1038\/35052548","volume":"2","author":"LA Pennacchio","year":"2001","unstructured":"Pennacchio LA, Rubin EM: Genomic strategies to identify mammalian regulatory sequences. Nat Rev Genet 2001, 2(2):100\u2013109. 10.1038\/35052548","journal-title":"Nat Rev Genet"},{"key":"2916_CR2","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1146\/annurev.genom.3.031302.100922","volume":"3","author":"V Reinke","year":"2002","unstructured":"Reinke V, White KP: Developmental genomic approaches in model organisms. Annu Rev Genomics Hum Genet 2002, 3: 153\u2013178. 10.1146\/annurev.genom.3.031302.100922","journal-title":"Annu Rev Genomics Hum Genet"},{"issue":"5235","key":"2916_CR3","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1126\/science.270.5235.467","volume":"270","author":"M Schena","year":"1995","unstructured":"Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270(5235):467\u2013470. 10.1126\/science.270.5235.467","journal-title":"Science"},{"issue":"7074","key":"2916_CR4","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1038\/nature04296","volume":"439","author":"AH Bild","year":"2006","unstructured":"Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D, Joshi MB, Harpole D, Lancaster JM, Berchuck A, Olson JA Jr, Marks JR, Dressman HK, West M, Nevins JR: Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 2006, 439(7074):353\u2013357. 10.1038\/nature04296","journal-title":"Nature"},{"issue":"5439","key":"2916_CR5","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1126\/science.286.5439.531","volume":"286","author":"TR Golub","year":"1999","unstructured":"Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286(5439):531\u2013537. 10.1126\/science.286.5439.531","journal-title":"Science"},{"issue":"7027","key":"2916_CR6","doi-asserted-by":"publisher","first-page":"769","DOI":"10.1038\/nature03315","volume":"433","author":"LP Lim","year":"2005","unstructured":"Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM: Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 2005, 433(7027):769\u2013773. 10.1038\/nature03315","journal-title":"Nature"},{"issue":"9","key":"2916_CR7","doi-asserted-by":"publisher","first-page":"1115","DOI":"10.1038\/nbt1236","volume":"24","author":"RD Canales","year":"2006","unstructured":"Canales RD, Luo Y, Willey JC, Austermiller B, Barbacioru CC, Boysen C, Hunkapiller K, Jensen RV, Knight CR, Lee KY, Ma Y, Maqsodi B, Papallo A, Peters EH, Poulter K, Ruppel PL, Samaha RR, Shi L, Yang W, Zhang L, Goodsaid FM: Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol 2006, 24(9):1115\u20131122. 10.1038\/nbt1236","journal-title":"Nat Biotechnol"},{"issue":"9","key":"2916_CR8","doi-asserted-by":"publisher","first-page":"1162","DOI":"10.1038\/nbt1238","volume":"24","author":"L Guo","year":"2006","unstructured":"Guo L, Lobenhofer EK, Wang C, Shippy R, Harris SC, Zhang L, Mei N, Chen T, Herman D, Goodsaid FM, Hurban P, Phillips KL, Xu J, Deng X, Sun YA, Tong W, Dragan YP, Shi L: Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat Biotechnol 2006, 24(9):1162\u20131169. 10.1038\/nbt1238","journal-title":"Nat Biotechnol"},{"issue":"9","key":"2916_CR9","doi-asserted-by":"publisher","first-page":"1140","DOI":"10.1038\/nbt1242","volume":"24","author":"TA Patterson","year":"2006","unstructured":"Patterson TA, Lobenhofer EK, Fulmer-Smentek SB, Collins PJ, Chu TM, Bao W, Fang H, Kawasaki ES, Hager J, Tikhonova IR, Walker SJ, Zhang L, Hurban P, de Longueville F, Fuscoe JC, Tong W, Shi L, Wolfinger RD: Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol 2006, 24(9):1140\u20131150. 10.1038\/nbt1242","journal-title":"Nat Biotechnol"},{"issue":"9","key":"2916_CR10","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1038\/nbt1239","volume":"24","author":"L Shi","year":"2006","unstructured":"Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JM, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Slikker W Jr, Shi L, Reid LH: The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006, 24(9):1151\u20131161. 10.1038\/nbt1239","journal-title":"Nat Biotechnol"},{"issue":"9","key":"2916_CR11","doi-asserted-by":"publisher","first-page":"1123","DOI":"10.1038\/nbt1241","volume":"24","author":"R Shippy","year":"2006","unstructured":"Shippy R, Fulmer-Smentek S, Jensen RV, Jones WD, Wolber PK, Johnson CD, Pine PS, Boysen C, Guo X, Chudin E, Sun YA, Willey JC, Thierry-Mieg J, Thierry-Mieg D, Setterquist RA, Wilson M, Lucas AB, Novoradovskaya N, Papallo A, Turpaz Y, Baker SC, Warrington JA, Shi L, Herman D: Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nat Biotechnol 2006, 24(9):1123\u20131131. 10.1038\/nbt1241","journal-title":"Nat Biotechnol"},{"issue":"9","key":"2916_CR12","doi-asserted-by":"publisher","first-page":"1132","DOI":"10.1038\/nbt1237","volume":"24","author":"W Tong","year":"2006","unstructured":"Tong W, Lucas AB, Shippy R, Fan X, Fang H, Hong H, Orr MS, Chu TM, Guo X, Collins PJ, Sun YA, Wang SJ, Bao W, Wolfinger RD, Shchegrova S, Guo L, Warrington JA, Shi L: Evaluation of external RNA controls for the assessment of microarray performance. Nat Biotechnol 2006, 24(9):1132\u20131139. 10.1038\/nbt1237","journal-title":"Nat Biotechnol"},{"issue":"5","key":"2916_CR13","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(5):345\u2013350. 10.1038\/nmeth756","journal-title":"Nat Methods"},{"issue":"7","key":"2916_CR14","doi-asserted-by":"publisher","first-page":"832","DOI":"10.1038\/nbt1217","volume":"24","author":"WP Kuo","year":"2006","unstructured":"Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone JR, Burke J, Park DJ, Wang X, Rector TL, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim JH, Short GF 3rd, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TK: A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol 2006, 24(7):832\u2013840. 10.1038\/nbt1217","journal-title":"Nat Biotechnol"},{"issue":"5","key":"2916_CR15","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1038\/nmeth757","volume":"2","author":"JE Larkin","year":"2005","unstructured":"Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J: Independence and reproducibility across microarray platforms. Nat Methods 2005, 2(5):337\u2013344. 10.1038\/nmeth757","journal-title":"Nat Methods"},{"issue":"9","key":"2916_CR16","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1038\/nbt0906-1105","volume":"24","author":"FW Frueh","year":"2006","unstructured":"Frueh FW: Impact of microarray data quality on genomic data submissions to the FDA. Nat Biotechnol 2006, 24(9):1105\u20131107. 10.1038\/nbt0906-1105","journal-title":"Nat Biotechnol"},{"issue":"9","key":"2916_CR17","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1038\/nrd1499","volume":"3","author":"LJ Lesko","year":"2004","unstructured":"Lesko LJ, Woodcock J: Translation of pharmacogenomics and pharmacogenetics: a regulatory perspective. Nat Rev Drug Discov 2004, 3(9):763\u2013769. 10.1038\/nrd1499","journal-title":"Nat Rev Drug Discov"},{"issue":"8","key":"2916_CR18","doi-asserted-by":"publisher","first-page":"1153","DOI":"10.2217\/14622416.7.8.1153","volume":"7","author":"G Hardiman","year":"2006","unstructured":"Hardiman G: Microarrays Technologies 2006: an overview. Pharmacogenomics 2006, 7(8):1153\u20131158. 10.2217\/14622416.7.8.1153","journal-title":"Pharmacogenomics"},{"issue":"3","key":"2916_CR19","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1038\/nrg1809","volume":"7","author":"JD Hoheisel","year":"2006","unstructured":"Hoheisel JD: Microarray technology: beyond transcript profiling and genotype analysis. Nat Rev Genet 2006, 7(3):200\u2013210. 10.1038\/nrg1809","journal-title":"Nat Rev Genet"},{"key":"2916_CR20","first-page":"D61","volume-title":"Nucleic Acids Res","author":"KD Pruitt","year":"2007","unstructured":"Pruitt KD, Tatusova T, Maglott DR: NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, (35 Database):D61\u201365. 10.1093\/nar\/gkl842"},{"issue":"20","key":"2916_CR21","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(20):e175. 10.1093\/nar\/gni179","journal-title":"Nucleic Acids Res"},{"key":"2916_CR22","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1186\/1756-0500-1-66","volume":"1","author":"WC de Leeuw","year":"2008","unstructured":"de Leeuw WC, Rauwerda H, Jonker MJ, Breit TM: Salvaging Affymetrix probes after probe-level re-annotation. BMC Res Notes 2008, 1: 66. 10.1186\/1756-0500-1-66","journal-title":"BMC Res Notes"},{"key":"2916_CR23","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1186\/1471-2105-8-446","volume":"8","author":"F Ferrari","year":"2007","unstructured":"Ferrari F, Bortoluzzi S, Coppe A, Sirota A, Safran M, Shmoish M, Ferrari S, Lancet D, Danieli GA, Bicciato S: Novel definition files for human GeneChips based on GeneAnnot. BMC Bioinformatics 2007, 8: 446. 10.1186\/1471-2105-8-446","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"2916_CR24","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(3):e31. 10.1093\/nar\/gni027","journal-title":"Nucleic Acids Res"},{"key":"2916_CR25","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1186\/1471-2105-10-30","volume":"10","author":"BHvan den Berg","year":"2009","unstructured":"Berg BH, Konieczka JH, McCarthy FM, Burgess SC: ArrayIDer: automated structural re-annotation pipeline for DNA microarrays. BMC Bioinformatics 2009, 10: 30. 10.1186\/1471-2105-10-30","journal-title":"BMC Bioinformatics"},{"issue":"11","key":"2916_CR26","doi-asserted-by":"publisher","first-page":"6931","DOI":"10.4049\/jimmunol.178.11.6931","volume":"178","author":"S Classen","year":"2007","unstructured":"Classen S, Zander T, Eggle D, Chemnitz JM, Brors B, Buchmann I, Popov A, Beyer M, Eils R, Debey S, S chultzeJL: Human resting CD4+ T cells are constitutively inhibited by TGF beta under steady-state conditions. J Immunol 2007, 178(11):6931\u20136940.","journal-title":"J Immunol"},{"issue":"25","key":"2916_CR27","doi-asserted-by":"publisher","first-page":"1999","DOI":"10.1056\/NEJMoa021967","volume":"347","author":"MJvan de Vijver","year":"2002","unstructured":"Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, Parrish M, Atsma D, Witteve A, Glas en A, Delahaye L, Velde T, Bartelink H, Rodenhuis S, Rutgers ET, Friend SH, Bernards R: A gene-expression signature as a predictor of survival in breast cancer. The New England journal of medicine 2002, 347(25):1999\u20132009. 10.1056\/NEJMoa021967","journal-title":"The New England journal of medicine"},{"issue":"6871","key":"2916_CR28","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1038\/415530a","volume":"415","author":"LJ van't Veer","year":"2002","unstructured":"van't Veer LJ, Dai H, Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH: Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415(6871):530\u2013536. 10.1038\/415530a","journal-title":"Nature"},{"key":"2916_CR29","volume-title":"The NCBI Handbook","author":"J Pontius","year":"2003","unstructured":"Pontius J, Wagner L, Schuler G: UniGene: a unified view of the transcriptome. In The NCBI Handbook. Bethesda, MD: National Center for Biotechnology Information; 2003."},{"key":"2916_CR30","first-page":"D707","volume-title":"Nucleic acids research","author":"P Flicek","year":"2008","unstructured":"Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella AJ, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJ, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S: Ensembl 2008. Nucleic acids research 2008, (36 Database):D707\u201314."},{"key":"2916_CR31","first-page":"D16","volume-title":"Nucleic acids research","author":"DA Benson","year":"2006","unstructured":"Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL: GenBank. Nucleic acids research 2006, (34 Database):D16\u201320. 10.1093\/nar\/gkj157"},{"issue":"2","key":"2916_CR32","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1084\/jem.149.2.297","volume":"149","author":"OT Avery","year":"1979","unstructured":"Avery OT, MacLeod CM, McCarty M: Studies on the chemical nature of the substance inducing transformation of pneumococcal types. Inductions of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. J Exp Med 1979, 149(2):297\u2013326. 10.1084\/jem.149.2.297","journal-title":"J Exp Med"},{"issue":"1","key":"2916_CR33","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1586\/14789450.1.1.19","volume":"1","author":"MN Kronick","year":"2004","unstructured":"Kronick MN: Creation of the whole human genome microarray. Expert review of proteomics 2004, 1(1):19\u201328. 10.1586\/14789450.1.1.19","journal-title":"Expert review of proteomics"},{"issue":"11","key":"2916_CR34","doi-asserted-by":"publisher","first-page":"2347","DOI":"10.1101\/gr.2739104","volume":"14","author":"K Kuhn","year":"2004","unstructured":"Kuhn K, Baker SC, Chudin E, Lieu MH, Oeser S, Bennett H, Rigault P, Barker D, McDaniel TK, Chee MS: A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res 2004, 14(11):2347\u20132356. 10.1101\/gr.2739104","journal-title":"Genome Res"},{"issue":"7","key":"2916_CR35","doi-asserted-by":"publisher","first-page":"1701","DOI":"10.1084\/jem.20060772","volume":"203","author":"W Liu","year":"2006","unstructured":"Liu W, Putnam AL, Xu-Yu Z, Szot GL, Lee MR, Zhu S, Gottlieb PA, Kapranov P, Gingeras TR, Fazekas de St Groth B, Clayberger C, Soper DM, Ziegler SF, Bluestone JA: CD127 expression inversely correlates with FoxP3 and suppressive function of human CD4+ T reg cells. J Exp Med 2006, 203(7):1701\u20131711. 10.1084\/jem.20060772","journal-title":"J Exp Med"},{"issue":"7","key":"2916_CR36","doi-asserted-by":"publisher","first-page":"1693","DOI":"10.1084\/jem.20060468","volume":"203","author":"N Seddiki","year":"2006","unstructured":"Seddiki N, Santner-Nanan B, Martinson J, Zaunders J, Sasson S, Landay A, Solomon M, Selby W, Alexander SI, Nanan R, Kelleher A, Fazekas de St Groth B: Expression of interleukin (IL)-2 and IL-7 receptors discriminates between human regulatory and activated T cells. J Exp Med 2006, 203(7):1693\u20131700. 10.1084\/jem.20060468","journal-title":"J Exp Med"},{"key":"2916_CR37","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1186\/1471-2164-8-284","volume":"8","author":"JC Lee","year":"2007","unstructured":"Lee JC, Stiles D, Lu J, Cam MC: A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences. BMC Genomics 2007, 8: 284. 10.1186\/1471-2164-8-284","journal-title":"BMC Genomics"},{"key":"2916_CR38","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Development Core Team","year":"2007","unstructured":"R Development Core Team: R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing; 2007."},{"issue":"10","key":"2916_CR39","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(10):R80. 10.1186\/gb-2004-5-10-r80","journal-title":"Genome Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-186.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,31]],"date-time":"2021-08-31T21:39:30Z","timestamp":1630445970000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-186"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,6,18]]},"references-count":39,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["2916"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-186","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,6,18]]},"assertion":[{"value":"8 December 2008","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 June 2009","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 June 2009","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"186"}}