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 ChIPchip data across experiments and across different microarray platforms. The package provides functions for data import, quality assessment, data visualiza...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Benedikt Zacher, Pei Fen Kuan, Achim Tresch
• Keywords: BMCBI 2010, ChIP Signals, Genomic, Microarray Probe