Genome-Wide Mapping of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Microarray Hybridization (ChIP-chip). Part B: ChIP-chip Data Analysis

  • Ulrike Göbel
  • Julia Reimer
  • Franziska TurckEmail author
Part of the Methods in Molecular Biology™ book series (MIMB, volume 631)


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.

Key words

ChIPR ChIP-chip The R statistical programming language Preprocessing Target identification Cross-annotation 


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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Max Planck Institute for Plant Breeding ResearchKölnGermany

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