Statistical Models of Global Transcription Regulatory Mechanisms in Cancer

• Activity Number: 87
• Type: Invited
• Date/Time: Monday, July 30, 2007 : 8:30 AM to 10:20 AM
• Sponsor: General Methodology
• Author(s): Wei Li*+ and Xiaole S. Liu*
• Companies: Harvard School of Public Health and Dana-Farber Cancer Institute
• Keywords: genome tiling microarrays ; model-based analysis ; transcription regulation ; cistrome ; ChIP-chip

Abstract

Chromatin Immunoprecipitation coupled with DNA microarray analysis (ChIP-chip) is a popular technique to study cistromes, the set of cis-acting targets of a trans-acting factor on a genome scale. We developed a series of algorithms for the analysis of ChIP-chip on genome tiling microarrays, including a Microarray Blob Remover (MBR) to filter probes in blob defects on the array, an algorithm for eXtreme fast MApping of Nucleotide (XMAN) probes to the genome, a Model-based Analysis of Tiling arrays (MAT) that models probe baseline behavior from probe sequence and genome copy numbers, and a web Cis-Element Annotation System (CEAS) for a comprehensive annotation of protein-bound ChIP-regions in the genome. We applied these algorithms to the ChIP-chip data of Estrogen Receptor (ER) and Androgen Receptor (AR) on Affymetrix whole human genome tiling arrays to identify their cistromes.