A Statistical Model for Investigating Binding Probabilities of DNA Nucleotide Sequences Using Microarrays

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Abstract
Summary. There is considerable scientific interest in knowing the probability that a site‐specific transcription factor will bind to a given DNA sequence. Microarray methods provide an effective means for assessing the binding affinities of a large number of DNA sequences as demonstrated by Bulyk et al. (2001, Proceedings of the National Academy of Sciences, USA98, 7158–7163) in their study of the DNA‐binding specificities of Zif268 zinc fingers using microarray technology. In a follow‐up investigation, Bulyk, Johnson, and Church (2002, Nucleic Acid Research30, 1255–1261) studied the interdependence of nucleotides on the binding affinities of transcription proteins. Our article is motivated by this pair of studies. We present a general statistical methodology for analyzing microarray intensity measurements reflecting DNA‐protein interactions. The log probability of a protein binding to a DNA sequence on an array is modeled using a linear ANOVA model. This model is convenient because it employs familiar statistical concepts and procedures and also because it is effective for investigating the probability structure of the binding mechanism.