title: BayesPeak: Bayesian analysis of ChIP-seq data.
abstract: BACKGROUND
  High-throughput sequencing technology has become popular and widely used to study protein and DNA interactions. Chromatin immunoprecipitation, followed by sequencing of the resulting samples, produces large amounts of data that can be used to map genomic features such as transcription factor binding sites and histone modifications.
  
  
  METHODS
  Our proposed statistical algorithm, BayesPeak, uses a fully Bayesian hidden Markov model to detect enriched locations in the genome. The structure accommodates the natural features of the Solexa/Illumina sequencing data and allows for overdispersion in the abundance of reads in different regions. Moreover, a control sample can be incorporated in the analysis to account for experimental and sequence biases. Markov chain Monte Carlo algorithms are applied to estimate the posterior distributions of the model parameters, and posterior probabilities are used to detect the sites of interest.
  
  
  CONCLUSIONS
  We have presented a flexible approach for identifying peaks from ChIP-seq reads, suitable for use on both transcription factor binding and histone modification data. Our method estimates probabilities of enrichment that can be used in downstream analysis. The method is assessed using experimentally verified data and is shown to provide high-confidence calls with low false positive rates.
authors.affiliation: Statistical Laboratory, Centre for Mathematical Sciences, Wilberforce Road, Cambridge, UK. C.Spyrou@statslab.cam.ac.uk
authors.forename: Christiana
authors.initials: C
authors.lastname: Spyrou
authors.forename: Rory
authors.initials: R
authors.lastname: Stark
authors.forename: Andy G
authors.initials: AG
authors.lastname: Lynch
authors.forename: Simon
authors.initials: S
authors.lastname: Tavaré
mesh_terms: D001499:Bayes Theorem; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D011506:Proteins / Q000378:metabolism
chemical_list: D011506:Proteins; D004247:DNA