Data and text mining Advance Access publication March 1, 2013 ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data

Motivation: Although chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) or tiling array hybridization (ChIP-chip) is increasingly used to map genome-wide–binding sites of transcription factors (TFs), it still remains difficult to generate a qual-ity ChIPx (i.e. ChIP-seq or ChIP-chip) dataset because of the tremen-dous amount of effort required to develop effective antibodies and efficient protocols. Moreover, most laboratories are unable to easily obtain ChIPx data for one or more TF(s) in more than a handful of biological contexts. Thus, standard ChIPx analyses primarily focus on analyzing data from one experiment, and the discoveries are restricted to a specific biological context. Results: We propose to enrich this existing data analysis paradigm by developing a novel approach, ChIP-PED, which superimposes ChIPx data on large amounts of publicly available human and mouse gen