ChIP-chip: data, model, and analysis.
|Title||ChIP-chip: data, model, and analysis.|
|Publication Type||Journal Article|
|Year of Publication||2007|
|Authors||Zheng M, Barrera LO, Ren B, Wu Y|
|Date Published||2007 Sep|
|Keywords||Algorithms, Chromatin Immunoprecipitation, Computer Simulation, Data Interpretation, Statistical, Databases, Factual, DNA, DNA-Binding Proteins, Information Storage and Retrieval, Models, Genetic, Models, Statistical, Oligonucleotide Array Sequence Analysis|
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.