title: Toward breaking the histone code: bayesian graphical models for histone modifications.
abstract: BACKGROUND
  Histones are proteins that wrap DNA around in small spherical structures called nucleosomes. Histone modifications (HMs) refer to the post-translational modifications to the histone tails. At a particular genomic locus, each of these HMs can either be present or absent, and the combinatory patterns of the presence or absence of multiple HMs, or the histone codes, are believed to coregulate important biological processes. We aim to use raw data on HM markers at different genomic loci to (1) decode the complex biological network of HMs in a single region, and (2) demonstrate how the HM networks differ in different regulatory regions. We suggest that these differences in network attributes form a significant link between histones and genomic functions.
  
  
  RESULTS
  We develop a powerful graphical model under the Bayesian paradigm. Posterior inference is fully probabilistic, allowing us to compute the probabilities of distinct dependence patterns of the HMs using graphs. Furthermore, our model-based framework allows for easy but important extensions for inference on differential networks under various conditions, such as the different annotations of the genomic locations (eg, promoters versus insulators). We applied these models to ChIP-Seq data based on CD4+ T lymphocytes. The results confirmed many existing findings and provided a unified tool to generate various promising hypotheses. Differential network analyses revealed new insights on coregulation of HMs of transcriptional activities in different genomic regions.
  
  
  CONCLUSIONS
  The use of Bayesian graphical models and borrowing strength across different conditions provide high power to infer histone networks and their differences.
authors.affiliation: ICES, University of Texas at Austin, USA.
authors.forename: Riten
authors.initials: R
authors.lastname: Mitra
authors.forename: Peter
authors.initials: P
authors.lastname: Müller
authors.forename: Shoudan
authors.initials: S
authors.lastname: Liang
authors.forename: Yanxun
authors.initials: Y
authors.lastname: Xu
authors.forename: Yuan
authors.initials: Y
authors.lastname: Ji
mesh_terms: D001499:Bayes Theorem; D015496:CD4-Positive T-Lymphocytes / Q000276:immunology / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D057890:Epigenomics; D042421:Histone Code; D006657:Histones / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D015233:Models, Statistical; D017422:Sequence Analysis, DNA
chemical_list: D006657:Histones
keywords: epigenomics; gene expression regulation; graph; models, statistical; network; nucleosomes; statistics