Göbel Ulrike, Reimer Julia, Turck Franziska
Max Planck Institute for Plant Breeding Research, Köln, Germany.
Methods Mol Biol. 2010;631:161-84. doi: 10.1007/978-1-60761-646-7_13.
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.
染色质相关因子的全基因组靶点可通过染色质免疫沉淀和寡核苷酸微阵列杂交相结合的方法来鉴定。全基因组微阵列数据分析对实验生物学家来说是一项重大挑战。本章介绍了ChIPR，这是一个用R统计编程语言编写的软件包，有助于分析来自罗氏- Nimblegen的双色微阵列。用拟南芥的样本数据说明了ChIPR的工作流程。然而，ChIPR支持ChIP-chip数据预处理、靶点识别以及对任何在GFF格式中具有基因组注释数据的物种进行交叉注释。本章描述了如何将ChIPR用作软件工具，而无需具备R语言的编程技能。
