Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

Background: High throughput signature sequencing holds many promises, one of which is the ready identification of in vivo transcription factor binding sites, histone modifications, changes in chromatin structure and patterns of DNA methylation across entire genomes. In these experiments, chromatin immunoprecipitation is used to enrich for particular DNA sequences of interest and signature sequencing is used to map the regions to the genome (ChIP-Seq). Elucidation of these sites of DNA-protein binding/modification are proving instrumental in reconstructing networks of gene regulation and chromatin remodelling that direct development, response to cellular perturbation, and neoplastic transformation. Results: Here we present a package of algorithms and software that makes use of control input data to reduce false positives and estimate confidence in ChIP-Seq peaks. Several different methods were compared using two simulated spike-in datasets. Use of control input data and a normalized di...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: David A. Nix, Samir J. Courdy, Kenneth M. Boucher
• Keywords: BMCBI 2008, Chromatin, Chromatin Immunoprecipitation, Control Input Data