title: Strategies for analyzing highly enriched IP-chip datasets.
abstract: BACKGROUND
  Chromatin immunoprecipitation on tiling arrays (ChIP-chip) has been employed to examine features such as protein binding and histone modifications on a genome-wide scale in a variety of cell types. Array data from the latter studies typically have a high proportion of enriched probes whose signals vary considerably (due to heterogeneity in the cell population), and this makes their normalization and downstream analysis difficult.
  
  
  RESULTS
  Here we present strategies for analyzing such experiments, focusing our discussion on the analysis of Bromodeoxyruridine (BrdU) immunoprecipitation on tiling array (BrdU-IP-chip) datasets. BrdU-IP-chip experiments map large, recently replicated genomic regions and have similar characteristics to histone modification/location data. To prepare such data for downstream analysis we employ a dynamic programming algorithm that identifies a set of putative unenriched probes, which we use for both within-array and between-array normalization. We also introduce a second dynamic programming algorithm that incorporates a priori knowledge to identify and quantify positive signals in these datasets.
  
  
  CONCLUSIONS
  Highly enriched IP-chip datasets are often difficult to analyze with traditional array normalization and analysis strategies. Here we present and test a set of analytical tools for their normalization and quantification that allows for accurate identification and analysis of enriched regions.
authors.affiliation: Molecular and Computational Biology Program, University of Southern California, Ray Irani Hall, University Park Campus, Los Angeles, CA 90089-2910, USA. knott@usc.edu
authors.forename: Simon R V
authors.initials: SR
authors.lastname: Knott
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Viggiani
authors.forename: Oscar M
authors.initials: OM
authors.lastname: Aparicio
authors.forename: Simon
authors.initials: S
authors.lastname: Tavaré
mesh_terms: D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D016247:Information Storage and Retrieval / Q000379:methods*