ChIP-chip: data, model, and analysis

Biometrics. 2007 Sep;63(3):787-96. 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.

MeSH terms

  • Algorithms*
  • Chromatin Immunoprecipitation / methods*
  • Computer Simulation
  • DNA / metabolism*
  • DNA-Binding Proteins / metabolism*
  • Data Interpretation, Statistical*
  • Databases, Factual
  • Information Storage and Retrieval / methods
  • Models, Genetic*
  • Models, Statistical
  • Oligonucleotide Array Sequence Analysis / methods*


  • DNA-Binding Proteins
  • DNA