Journal
BIOMETRICS
Volume 63, Issue 3, Pages 787-796Publisher
WILEY
DOI: 10.1111/j.1541-0420.2007.00768.x
Keywords
genome; peak detection; protein binding sites; sonication; truncated triangle shape model
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ChIP-chip (or ChIP-on-chip) is a technology for isolation and identification of genomic sites occupied by specific DNA-binding proteins in living cells. The ChIP-chip signals can be obtained over the whole genome by tiling arrays, where a peak shape is generally observed around a protein-binding site. In this article, we describe the ChIP-chip process and present a probability model for ChIP-chip data. We then propose a model-based method for recognizing the peak shapes for the purpose of detecting protein-binding sites. We also investigate the issue of bandwidth in nonparametric kernel smoothing method.
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