ChIP-chip: data, model, and 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.
Zheng
Ming
M
Department of Statistics, UCLA, 8125 Math Sciences Bldg, Los Angeles, California 90095-1554, USA.
Barrera
Leah O
LO
Ren
Bing
B
Wu
Ying Nian
YN
D000465:Algorithms; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D003198:Computer Simulation; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D003627:Data Interpretation, Statistical; D016208:Databases, Factual; D016247:Information Storage and Retrieval / Q000379:methods; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*