Normalization and experimental design for ChIP-chip data

Background: Chromatin immunoprecipitation on tiling arrays (ChIP-chip) has been widely used to investigate the DNA binding sites for a variety of proteins on a genome-wide scale. However, several issues in the processing and analysis of ChIP-chip data have not been resolved fully, including the effect of background (mock control) subtraction and normalization within and across arrays. Results: The binding profiles of Drosophila male-specific lethal (MSL) complex on a tiling array provide a unique opportunity for investigating these topics, as it is known to bind on the X chromosome but not on the autosomes. These large bound and control regions on the same array allow clear evaluation of analytical methods. We introduce a novel normalization scheme specifically designed for ChIP-chip data from dualchannel arrays and demonstrate that this step is critical for correcting systematic dye-bias that may exist in the data. Subtraction of the mock (non-specific antibody or no antibody) contro...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Shouyong Peng, Artyom A. Alekseyenko, Erica Larschan, Mitzi I. Kuroda, Peter J. Park
• Keywords: BMCBI 2007, ChIP-chip Data, Chromatin Immunoprecipitation, Genome-wide Scale