Starr

Starr is a software tool designed to analyze Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) data. ChIP-chip is a high-throughput technology investigating DNA-protein-binding or post-translational chromatin/histone modifications. However, it requires thorough bioinformatic processing of the data, for which there is no standard yet. The primary goal of ChIP-chip is to reliably identify and localize genomic regions that bind a specific protein. Further investigation then 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.

Starr is an open-source R/Bioconductor package that enables comparative analysis of ChIP-chip data across experiments and different microarray platforms. It is a free software tool that is focused on high-level data analysis. It facilitates 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.

Starr automatically updates microarray probe annotation files by efficiently remapping microarray probe sequences to an arbitrary genome. This feature ensures that the tool can be used across different microarray platforms. Importantly, Starr covers the complete ChIP-chip workflow from data processing to binding pattern detection. It provides methods for the integration and combined statistical analysis of binding profiles and complementary functional genomics data. This is valuable because it enables systematic assessment of binding behavior for gene groups aligned along arbitrary genomic features.