title: Using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.
abstract: Genome-wide mapping of nucleosomes has revealed a great deal about the relationships between chromatin structure and control of gene expression. Recent next generation CHIP-chip and CHIP-Seq technologies have accelerated our understanding of basic principles of chromatin organization. These technologies have taught us that nucleosomes play a crucial role in gene regulation by allowing physical access to transcription factors. Recent methods and experimental advancements allow the determination of nucleosome positions for a given genome area. However, most of these methods estimate the number of nucleosomes either by an EM algorithm using a BIC criterion or an effective heuristic strategy. Here, we introduce a Bayesian method for identifying nucleosome positions. The proposed model is based on a Multinomial-Dirichlet classification and a hierarchical mixture distributions. The number and the positions of nucleosomes are estimated using a reversible jump Markov chain Monte Carlo simulation technique. We compare the performance of our method on simulated data and MNase-Seq data from Saccharomyces cerevisiae against PING and NOrMAL methods.
authors.forename: Rawane
authors.initials: R
authors.lastname: Samb
authors.forename: Khader
authors.initials: K
authors.lastname: Khadraoui
authors.forename: Pascal
authors.initials: P
authors.lastname: Belleau
authors.forename: Astrid
authors.initials: A
authors.lastname: Deschênes
authors.forename: Lajmi
authors.initials: L
authors.lastname: Lakhal-Chaieb
authors.forename: Arnaud
authors.initials: A
authors.lastname: Droit
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D002874:Chromosome Mapping / Q000379:methods*; D016681:Genome, Fungal; D016013:Likelihood Functions; D008390:Markov Chains; D008957:Models, Genetic; D009010:Monte Carlo Method; D009707:Nucleosomes / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D009707:Nucleosomes