ChIP-chip: data, model, and analysis.

TitleChIP-chip: data, model, and analysis.
Publication TypeJournal Article
Year of Publication2007
AuthorsZheng M, Barrera LO, Ren B, Wu Y
JournalBiometrics
Volume63
Issue3
Pagination787-96
Date Published2007 Sep
ISSN0006-341X
KeywordsAlgorithms, 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
Abstract

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.

DOI10.1111/j.1541-0420.2007.00768.x
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/17825010?dopt=Abstract
Alternate JournalBiometrics
PubMed ID17825010