{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T13:00:32Z","timestamp":1773666032151,"version":"3.50.1"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: High-density DNA microarrays provide us with useful tools for analyzing DNA and RNA comprehensively. However, the background signal caused by the non-specific binding (NSB) between probe and target makes it difficult to obtain accurate measurements. To remove the background signal, there is a set of background probes on Affymetrix Exon arrays to represent the amount of non-specific signals, and an accurate estimation of non-specific signals using these background probes is desirable for improvement of microarray analyses.<\/jats:p>\n               <jats:p>Results: We developed a thermodynamic model of NSB on short nucleotide microarrays in which the NSBs are modeled by duplex formation of probes and multiple hypothetical targets. We fitted the observed signal intensities of the background probes with those expected by the model to obtain the model parameters. As a result, we found that the presented model can improve the accuracy of prediction of non-specific signals in comparison with previously proposed methods. This result will provide a useful method to correct for the background signal in oligonucleotide microarray analysis.<\/jats:p>\n               <jats:p>Availability: The software is implemented in the R language and can be downloaded from our website (http:\/\/www-shimizu.ist.osaka-u.ac.jp\/shimizu_lab\/MSNS\/).<\/jats:p>\n               <jats:p>Contact: \u00a0furusawa@ist.osaka-u.ac.jp<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn570","type":"journal-article","created":{"date-parts":[[2008,11,1]],"date-time":"2008-11-01T00:24:42Z","timestamp":1225499082000},"page":"36-41","source":"Crossref","is-referenced-by-count":17,"title":["Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays"],"prefix":"10.1093","volume":"25","author":[{"given":"Chikara","family":"Furusawa","sequence":"first","affiliation":[{"name":"1 Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2Complex Systems Biology Project, ERATO and 3Graduate School of Frontier Biosciences, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan"},{"name":"1 Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2Complex Systems Biology Project, ERATO and 3Graduate School of Frontier Biosciences, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Naoaki","family":"Ono","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2Complex Systems Biology Project, ERATO and 3Graduate School of Frontier Biosciences, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shingo","family":"Suzuki","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2Complex Systems Biology Project, ERATO and 3Graduate School of Frontier Biosciences, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tomoharu","family":"Agata","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2Complex Systems Biology Project, ERATO and 3Graduate School of Frontier Biosciences, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hiroshi","family":"Shimizu","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2Complex Systems Biology Project, ERATO and 3Graduate School of Frontier Biosciences, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tetsuya","family":"Yomo","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2Complex Systems Biology Project, ERATO and 3Graduate School of Frontier Biosciences, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan"},{"name":"1 Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2Complex Systems Biology Project, ERATO and 3Graduate School of Frontier Biosciences, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan"},{"name":"1 Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2Complex Systems Biology Project, ERATO and 3Graduate School of Frontier Biosciences, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,10,31]]},"reference":[{"key":"2023013110022899800_B1","article-title":"New Statistical Algorithms for Monitoring Gene Expression on GeneChip Probe Arrays","volume-title":"Technical Note. Affymetrix.","author":"Affymetrix","year":"2001"},{"key":"2023013110022899800_B2","article-title":"Exon Array Background Correction","volume-title":"Technical Note. Affymetrix.","author":"Affymetrix","year":"2005"},{"key":"2023013110022899800_B3","doi-asserted-by":"crossref","first-page":"2242","DOI":"10.1126\/science.1103388","article-title":"Global identification of human transcribed sequences with genome tiling arrays","volume":"306","author":"Bertone","year":"2004","journal-title":"Science"},{"key":"2023013110022899800_B4","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1016\/j.ygeno.2003.11.004","article-title":"ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments","volume":"83","author":"Buck","year":"2003","journal-title":"Genomics"},{"key":"2023013110022899800_B5","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1093\/bioinformatics\/btg410","article-title":"A benchmark for Affymetrix genechip expression measures","volume":"20","author":"Cope","year":"2004","journal-title":"Bioinformatics"},{"key":"2023013110022899800_B6","doi-asserted-by":"crossref","first-page":"088102","DOI":"10.1103\/PhysRevLett.90.088102","article-title":"Zipf's law in gene expression","volume":"90","author":"Furusawa","year":"2003","journal-title":"Phys. Rev. Lett."},{"key":"2023013110022899800_B7","doi-asserted-by":"crossref","first-page":"e70","DOI":"10.1093\/nar\/gkl122","article-title":"Relationship between gene expression and observed intensities in DNA microarrays\u2013a modeling study","volume":"34","author":"Held","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023013110022899800_B8","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1093\/bioinformatics\/btk046","article-title":"Comparison of Affymetrix genechip expression measures","volume":"22","author":"Irizarry","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013110022899800_B9","doi-asserted-by":"crossref","first-page":"12457","DOI":"10.1073\/pnas.0601180103","article-title":"Model-based analysis of tiling-arrays for ChIP-chip","volume":"103","author":"Johson","year":"2006","journal-title":"Proc. Natl Acad. Sci."},{"key":"2023013110022899800_B10","doi-asserted-by":"crossref","first-page":"R82","DOI":"10.1186\/gb-2007-8-5-r82","article-title":"Exon arrays provide accurate assessments of gene expression","volume":"8","author":"Kapur","year":"2007","journal-title":"Genome Biol."},{"key":"2023013110022899800_B11","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1073\/pnas.98.1.31","article-title":"Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection","volume":"98","author":"Li","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023013110022899800_B12","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1038\/4447","article-title":"High density synthetic oligonucleotide arrays","volume":"21","author":"Lipshutz","year":"1999","journal-title":"Nat. Genet."},{"key":"2023013110022899800_B13","doi-asserted-by":"crossref","first-page":"W577","DOI":"10.1093\/nar\/gki591","article-title":"Dinamelt web server for nucleic acid melting prediction","volume":"33","author":"Markham","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023013110022899800_B14","doi-asserted-by":"crossref","first-page":"4211","DOI":"10.1093\/nar\/gkg476","article-title":"Thermodynamic calculations and statistical correlations for oligo-probes design","volume":"31","author":"Matveeva","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023013110022899800_B15","doi-asserted-by":"crossref","first-page":"011906","DOI":"10.1103\/PhysRevE.68.011906","article-title":"Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays","volume":"68","author":"Naef","year":"2003","journal-title":"Phys. Rev. E Stat. Nonlin. Soft. Matter Phys."},{"key":"2023013110022899800_B16","doi-asserted-by":"crossref","first-page":"040902","DOI":"10.1103\/PhysRevE.65.040902","article-title":"DNA hybridization to mismatched templates: a chip study","volume":"65","author":"Naef","year":"2002","journal-title":"Phys. Rev. E"},{"key":"2023013110022899800_B17","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1093\/bioinformatics\/btn109","article-title":"An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays","volume":"24","author":"Ono","year":"2008","journal-title":"Bioinformatics"},{"key":"2023013110022899800_B18","article-title":"R: A Language and Environment for Statistical Computing","volume-title":"R Foundation for Statistical Computing","author":"R Development Core Team","year":"2006"},{"key":"2023013110022899800_B19","doi-asserted-by":"crossref","first-page":"1460","DOI":"10.1073\/pnas.95.4.1460","article-title":"A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics","volume":"95","author":"SantaLucia","year":"1998","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013110022899800_B20","doi-asserted-by":"crossref","first-page":"R216","DOI":"10.1186\/gb-2007-8-6-r126","article-title":"Estimation and correction of non-specific binding in a large-scale spike-in experiment","volume":"8","author":"Schuster","year":"2007","journal-title":"Genome Biol."},{"key":"2023013110022899800_B21","doi-asserted-by":"crossref","first-page":"1262","DOI":"10.1038\/82367","article-title":"RNA expression analysis using a 30 base pair resolution Escherichia Coli genome array","volume":"18","author":"Selinger","year":"2000","journal-title":"Nat. Biotechnol."},{"key":"2023013110022899800_B22","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1186\/1471-2164-5-61","article-title":"Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations","volume":"5","author":"Shippy","year":"2004","journal-title":"BMC Genomics"},{"key":"2023013110022899800_B23","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1186\/1471-2164-8-373","article-title":"Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays","volume":"8","author":"Suzuki","year":"2007","journal-title":"BMC Genomics"},{"key":"2023013110022899800_B24","doi-asserted-by":"crossref","first-page":"e84","DOI":"10.1093\/nar\/gni082","article-title":"Sequence dependence of cross-hybridization on short oligo microarrays","volume":"33","author":"Wu","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023013110022899800_B25","doi-asserted-by":"crossref","first-page":"2566","DOI":"10.1093\/bioinformatics\/btm271","article-title":"Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarray","volume":"23","author":"Wu","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013110022899800_B26","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1038\/nbt0604-656b","article-title":"Preprocessing of oligonucleotide array data","volume":"22","author":"Wu","year":"2004","journal-title":"Nat. Biotechnol."},{"key":"2023013110022899800_B27","doi-asserted-by":"crossref","first-page":"e48","DOI":"10.1093\/nar\/30.10.e48","article-title":"Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays","volume":"30","author":"Yuen","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023013110022899800_B28","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1038\/nbt836","article-title":"A model of molecular interactions on short oligonucleotide microarrays","volume":"21","author":"Zhang","year":"2003","journal-title":"Nat. Biotechnol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/1\/36\/48982106\/bioinformatics_25_1_36.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/1\/36\/48982106\/bioinformatics_25_1_36.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T18:51:00Z","timestamp":1675191060000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/1\/36\/301998"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,10,31]]},"references-count":28,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn570","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,1,1]]},"published":{"date-parts":[[2008,10,31]]}}}