title: Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays.
abstract: BACKGROUND
  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.
  
  
  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.
  
  
  BACKGROUND
  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/).
authors.affiliation: Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka 565-0871, Japan. furusawa@ist.osaka-u.ac.jp
authors.forename: Chikara
authors.initials: C
authors.lastname: Furusawa
authors.forename: Naoaki
authors.initials: N
authors.lastname: Ono
authors.forename: Shingo
authors.initials: S
authors.lastname: Suzuki
authors.forename: Tomoharu
authors.initials: T
authors.lastname: Agata
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Shimizu
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Yomo
mesh_terms: D016477:Artifacts; D020137:Base Pair Mismatch; D019295:Computational Biology; D015342:DNA Probes; D006801:Humans; D008954:Models, Biological; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*
chemical_list: D015342:DNA Probes