Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data

Background: Chromatin immunoprecipitation combined with DNA
microarrays (ChIP-chip) is an assay used for investigating
DNA-protein-binding or post-translational chromatin/histone
modifications. As with all high-throughput technologies, it
requires thorough bioinformatic processing of the data for which
there is no standard yet. The primary goal is to reliably identify
and localize genomic regions that bind a specific protein. Further
investigation compares binding profiles of functionally related
proteins, or binding profiles of the same proteins in different
genetic backgrounds or experimental conditions. Ultimately, the
goal is to gain a mechanistic understanding of the effects of DNA
binding events on gene expression. Results: We present a free,
open-source R/Bioconductor package Starr that facilitates
comparative analysis of ChIP-chip data across experiments and
across different microarray platforms. The package provides
functions for data import, quality assessment, data visualization
and exploration. Starr includes high-level analysis tools such as
the alignment of ChIP signals along annotated features, correlation
analysis of ChIP signals with complementary genomic data,
peak-finding and comparative display of multiple clusters of
binding profiles. It uses standard Bioconductor classes for maximum
compatibility with other software. Moreover, Starr automatically
updates microarray probe annotation files by a highly efficient
remapping of microarray probe sequences to an arbitrary genome.
Conclusion: Starr is an R package that covers the complete
ChIP-chip workflow from data processing to binding pattern
detection. It focuses on the high-level data analysis, e. g., it
provides methods for the integration and combined statistical
analysis of binding profiles and complementary functional genomics
data. Starr enables systematic assessment of binding behaviour for
groups of genes that are alingned along arbitrary genomic features.