ChIP-chip: Data, Model, and Analysis
Article first published online: 20 MAR 2007
Volume 63, Issue 3, pages 787–796, September 2007
How to Cite
Zheng, M., Barrera, L. O., Ren, B. and Wu, Y. N. (2007), ChIP-chip: Data, Model, and Analysis. Biometrics, 63: 787–796. doi: 10.1111/j.1541-0420.2007.00768.x
- Issue published online: 20 MAR 2007
- Article first published online: 20 MAR 2007
- Received October 2005. Revised November 2006. Accepted November 2006.
- Peak detection;
- Protein binding sites;
- Truncated triangle shape model
Summary 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.