3d International ICST Conference on Bio-Inspired Models of Network, Information, and Computing Systems

Research Article

Quantitative expression analysis using oligonucleotide microarrays based on a physico-chemical model

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  • @INPROCEEDINGS{10.4108/ICST.BIONETICS2008.4750,
        author={Naoaki Ono and Shingo Suzuki and Chikara Furusawa and Hiroshi Shimizu and Tetsuya Yomo},
        title={Quantitative expression analysis using oligonucleotide microarrays based on a physico-chemical model},
        proceedings={3d International ICST Conference on Bio-Inspired Models of Network, Information, and Computing Systems},
        publisher={ICST},
        proceedings_a={BIONETICS},
        year={2010},
        month={5},
        keywords={microarray expression analysis},
        doi={10.4108/ICST.BIONETICS2008.4750}
    }
    
  • Naoaki Ono
    Shingo Suzuki
    Chikara Furusawa
    Hiroshi Shimizu
    Tetsuya Yomo
    Year: 2010
    Quantitative expression analysis using oligonucleotide microarrays based on a physico-chemical model
    BIONETICS
    ICST
    DOI: 10.4108/ICST.BIONETICS2008.4750
Naoaki Ono1,*, Shingo Suzuki1,*, Chikara Furusawa2,*, Hiroshi Shimizu1,*, Tetsuya Yomo3,*
  • 1: Graduate school of Information Science and Technology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
  • 2: Graduate school of Information Science and Technology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan ERATO, JST
  • 3: Graduate school of Information Science and Technology, Graduate School of Frontier Biosciences, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan ERATO, JST
*Contact email: nono@ist.osaka-u.ac.jp, shingo@ist.osaka-u.ac.jp, furusawa@ist.osaka-u.ac.jp, shimizu@ist.osak-u.ac.jp, yomo@ist.osaka-u.ac.jp

Abstract

High-density DNA microarrays provide useful tools to analyze gene expression comprehensively. However, it is still difficult to obtain accurate expression levels from the observed microarray data because the signal intensity is affected by complicated factors involving probe---target hybridization, such as nonlinear behavior of hybridization, nonspecific hybridization, and folding of probe and target oligonucleotides. Various methods for microarray data analysis have been proposed to address this problem. In our previous report [7], we presented a benchmark analysis of probe---target hybridization using artificially synthesized oligonucleotides as targets, in which effect of nonspecific hybridization was negligible. The results showed that the preceding models explained the behavior of probe---target hybridization only within a narrow range of target concentrations. The experiments showed that finiteness of both probe and target molecules should be considered to understand detail behavior of hybridization.

In this paper, we present an extension of the Langmuir-model that reproduces the experimental results consistently and the 3-base nearest neighbor model to improve prediction accuracy. We also introduced effects of secondary structure formation, and dissociation of the probe---target duplex during washing after hybridization. The results will provide useful methods for the understanding and analysis of microarray experiments.