Abstract
Genome-wide targets of chromatin-associated factors can be identified by a combination of chromatin-immunoprecipitation and oligonucleotide microarray hybridization. Genome-wide mircoarray data analysis represents a major challenge for the experimental biologist. This chapter introduces ChIPR, a package written in the R statistical programming language that facilitates the analysis of two-color microarrays from Roche-Nimblegen. The workflow of ChIPR is illustrated with sample data from Arabidopsis thaliana. However, ChIPR supports ChIP-chip data preprocessing, target identification, and cross-annotation of any species for which genome annotation data is available in GFF format. This chapter describes how to use ChIPR as a software tool without the requirement for programming skills in the R language.
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Göbel, U., Reimer, J., Turck, F. (2010). Genome-Wide Mapping of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Microarray Hybridization (ChIP-chip). Part B: ChIP-chip Data Analysis. In: Kovalchuk, I., Zemp, F. (eds) Plant Epigenetics. Methods in Molecular Biology™, vol 631. Humana Press. https://doi.org/10.1007/978-1-60761-646-7_13
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DOI: https://doi.org/10.1007/978-1-60761-646-7_13
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