Strategies for analyzing highly enriched IP-chip datasets

Knott, S. R., Viggiani, C. J., Aparicio, O. M., Tavare, S. (2009) Strategies for analyzing highly enriched IP-chip datasets. BMC Bioinformatics, 10. p. 305. ISSN 1471-2105

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DOI: 10.1186/1471-2105-10-305


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. CONCLUSION: 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.

Item Type: Paper
Uncontrolled Keywords: *Chromatin Immunoprecipitation Computational Biology/*methods Gene Expression Profiling Information Storage and Retrieval/*methods
Subjects: Investigative techniques and equipment
Investigative techniques and equipment > Chromatin immunoprecipitation
CSHL Authors:
Communities: CSHL Post Doctoral Fellows
CSHL labs > Hannon lab
Depositing User: Matt Covey
Date: 2009
Date Deposited: 18 Mar 2015 15:17
Last Modified: 18 Mar 2015 15:17
PMCID: PMC2759964
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