Genome Wide Mapping of Protein–DNA Interaction by Chromatin Immunoprecipitation and DNA Microarray Hybridization ChIP chip. Part B ChIP chip Data Analysis英文文献.pdfVIP

Chapter 13 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, and Franziska Turck 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. Key words: ChIPR, ChIP-chip, The R statistical programming language, Preprocessing, Target identification, Cross-annotation 1. Introduction ChIP-chip data are generated by the combination of chromatin immunprecipitation (ChIP) and oligonucleotide microarray mea- surements (chip). It is common practice to measure ChIP-chip data from two-color microarray platforms, which are simultaneously hybridized with a ChIP sample and a nonprecipitated input DNA as a reference. Samples are differentially labeled with fluorescent dyes, usually Cy3 and Cy5, which can