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A model of molecular interactions on short oligonucleotide microarrays

Nature Biotechnology volume 21, pages 818–821 (2003)Cite this article

A Corrigendum to this article was published on 01 August 2003

Abstract

High-density short oligonucleotide microarrays have become a widely used tool for measuring gene expression on a large scale1,2. However, details of the mechanism of binding on microarrays remain unclear3. Short oligonucleotide probes currently synthesized on microarrays are often ineffective as a result of limited sequence specificity or low sensitivity. Here, we describe a model of binding interactions on microarrays that reveals how probe signals depend on probe sequences and why certain probes are ineffective. The model indicates that the amount of nonspecific binding can be estimated from a simple rule. Using this model, we have developed an improved measure of gene expression for use in data analysis.

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Figure 1: Model fitting and parameterization.
Figure 2: Accuracy test.
Figure 3: Evaluating probe pair signals with PDNN model.

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Acknowledgements

We thank Keith Baggerly, Kevin R. Coombes, Kenneth Hess, Jan Hermans, Roberto Carta, Jing Wang, David Gold, LeeAnn Chastain and Zoltan Szallasi for suggestions on the manuscript and Nobert Wilke and Mini Kapoor for technical support. This work was supported by The University of Texas M.D. Anderson Cancer Center, a grant (DA14167) from the National Institute for Drug Abuse and funding from the State of California.

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Authors and Affiliations

  1. Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Blvd. 447, Houston, 77030, Texas, USA

    Li Zhang

  2. Departments of Pharmacology/Toxicology and Neurology and the Center for Study of Biological Complexity, Virginia Commonwealth University, Richmond, 23298-0599, Virginia, USA

    Michael F Miles

  3. Department of Pathology & Brain Tumor Center The University of Texas M.D. Anderson Cancer Center, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Blvd. 447, Houston, 77030, Texas, USA

    Kenneth D Aldape

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Correspondence to Li Zhang.

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Zhang, L., Miles, M. & Aldape, K. A model of molecular interactions on short oligonucleotide microarrays. Nat Biotechnol 21, 818–821 (2003). https://doi.org/10.1038/nbt836

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