ChIP-chip: Data, Model, and Analysis

• Published in: Biometrics Vol. 63; no. 3; pp. 787 - 796
• Main Authors: Zheng, Ming, Barrera, Leah O, Ren, Bing, Wu, Ying Nian
• Format: Journal Article
• Language: English
• Published: Malden, USA Blackwell Publishing Inc 01.09.2007; International Biometric Society; Blackwell Publishing Ltd
• Subjects: Algorithms; Autocorrelation; Binding sites; Biomedical research; Chromatin Immunoprecipitation - methods; Computer Simulation; Data Interpretation, Statistical; Data models; Data smoothing; Databases, Factual; DNA; DNA - metabolism; DNA-Binding Proteins - metabolism; Genome; Genomes; Genomics; Information Storage and Retrieval - methods; Local maximum; Modeling; Models, Genetic; Models, Statistical; Oligonucleotide Array Sequence Analysis - methods; Peak detection; Protein binding sites; Research methodology; Sonication; Statistical analysis; Statistical variance; Truncated triangle shape model
• ISSN: 0006-341X; 1541-0420
• DOI: 10.1111/j.1541-0420.2007.00768.x

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.