Genome-wide mapping of protein-DNA interaction by chromatin immunoprecipitation and DNA microarray hybridization (ChIP-chip). Part B: ChIP-chip data analysis.
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.
Göbel
Ulrike
U
Max Planck Institute for Plant Breeding Research, Köln, Germany.
Reimer
Julia
J
Turck
Franziska
F
D017360:Arabidopsis / Q000235:genetics*; D002843:Chromatin / Q000378:metabolism; D047369:Chromatin Immunoprecipitation / Q000379:methods; D018744:DNA, Plant / Q000378:metabolism; D030541:Databases, Genetic; D001330:Electronic Data Processing / Q000379:methods*; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010940:Plant Proteins / Q000378:metabolism; D011381:Programming Languages; D011485:Protein Binding; D012984:Software
D002843:Chromatin; D018744:DNA, Plant; D010940:Plant Proteins