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Abstract:
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DNA-binding proteins play a key role in human health and disease, yet our current understanding of these proteins is limited by our knowledge of their binding sites in the genome. Chromatin immunoprecipitation (ChIP) is a powerful tool for determining whether a given protein binds to a specific DNA sequence in vivo. Recently, we have seen the emergence of high throughput assays (tiling arrays, high-throughput sequencing) that query all of the non-repetitive genomic sequences of human and other eukaryotes. When combined with ChIP, these assays permit the unbiased mapping of in vivo DNA-protein binding sites across a given genome. During this talk, I will describe some of the statistical issues involved in the analysis of high throughput ChIP data and will present some of the work we have done to address these issues. I will use both ChIP-chip and ChIP-Seq data to illustrate our methods.
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