Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts

Abstract

Background: Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) is a high-throughput assay for DNA-protein-binding or post-translational chromatin/histone modifications. However, the raw microarray intensity readings themselves are not immediately useful to researchers, but require a number of bioinformatic analysis steps. Identified enriched regions need to be bioinformatically annotated and compared to related datasets by statistical methods.

Results: We present a free, open-source R package Ringo that facilitates the analysis of ChIP-chip experiments by providing functionality for data import, quality assessment, normalization and visualization of the data, and the detection of ChIP-enriched genomic regions.

Conclusion: Ringo integrates with other packages of the Bioconductor project, uses common data structures and is accompanied by ample documentation. It facilitates the construction of programmed analysis workflows, offers benefits in scalability, reproducibility and methodical scope of the analyses and opens up a broad selection of follow-up statistical and bioinformatic methods.

Figure 1

ChIP-chip analysis with Ringo. Workflow diagram displaying which steps of the analysis of ChIP-chip experiments are facilitated by Ringo.

Figure 2

Autocorrelation in ChIP-chip data. An example data set on histone-3-acetylation, which is provided as part of the software documentation, is used to demonstrate the package's autocorrelation plot. For each base-pair offset d, it assesses how strong the intensities of probes mapped to genomic positions x + d are correlated with the probe intensities at positions x. The computed correlation is plotted against the offset.

Figure 3

Visualization of ChIP-enriched genomic regions. Original and smoothed probe-wise fold-changes for histone-3-acetylation (H3ac) in the vicinity of the transcription start site of the Hand2 gene on chromosome 8. The bold ticks beneath the genomic coordinate axis indicate genomic positions at which microarray probes target the genome sequence.