title: Nonparametric Bayesian Bi-Clustering for Next Generation Sequencing Count Data.
abstract: Histone modifications (HMs) play important roles in transcription through post-translational modifications. Combinations of HMs, known as chromatin signatures, encode specific messages for gene regulation. We therefore expect that inference on possible clustering of HMs and an annotation of genomic locations on the basis of such clustering can contribute new insights about the functions of regulatory elements and their relationships to combinations of HMs. We propose a nonparametric Bayesian local clustering Poisson model (NoB-LCP) to facilitate posterior inference on two-dimensional clustering of HMs and genomic locations. The NoB-LCP clusters HMs into HM sets and lets each HM set define its own clustering of genomic locations. Furthermore, it probabilistically excludes HMs and genomic locations that are irrelevant to clustering. By doing so, the proposed model effectively identifies important sets of HMs and groups regulatory elements with similar functionality based on HM patterns.
authors.affiliation: Department of Statistics, Rice University, Houston, TX, U.S.A. ; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, U.S.A.
authors.forename: Yanxun
authors.initials: Y
authors.lastname: Xu
authors.affiliation: Department of Statistics, The Ohio State University, Columbus, Ohio, U.S.A.
authors.forename: Juhee
authors.initials: J
authors.lastname: Lee
authors.affiliation: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, U.S.A.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Yuan
authors.affiliation: Department of Mathematics, University of Texas Austin, Austin, TX, U.S.A.
authors.forename: Riten
authors.initials: R
authors.lastname: Mitra
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, U.S.A.
authors.forename: Shoudan
authors.initials: S
authors.lastname: Liang
authors.affiliation: Department of Mathematics, University of Texas Austin, Austin, TX, U.S.A.
authors.forename: Peter
authors.initials: P
authors.lastname: Müller
authors.affiliation: NorthShore University HealthSystem, Chicago, IL, U.S.A.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Ji
keywords: Bi-Clustering; ChIP-Seq; Histone modifications; Markov chain Monte Carlo; Nonparametric Bayes