title: Two-dimensional segmentation for analyzing Hi-C data.
abstract: BACKGROUND
  The spatial conformation of the chromosome has a deep influence on gene regulation and expression. Hi-C technology allows the evaluation of the spatial proximity between any pair of loci along the genome. It results in a data matrix where blocks corresponding to (self-)interacting regions appear. The delimitation of such blocks is critical to better understand the spatial organization of the chromatin. From a computational point of view, it results in a 2D segmentation problem.
  
  
  RESULTS
  We focus on the detection of cis-interacting regions, which appear to be prominent in observed data. We define a block-wise segmentation model for the detection of such regions. We prove that the maximization of the likelihood with respect to the block boundaries can be rephrased in terms of a 1D segmentation problem, for which the standard dynamic programming applies. The performance of the proposed methods is assessed by a simulation study on both synthetic and resampled data. A comparative study on public data shows good concordance with biologically confirmed regions.
  
  
  METHODS
  The HiCseg R package is available from the Comprehensive R Archive Network and from the Web page of the corresponding author.
authors.affiliation: AgroParisTech/INRA MIA 518, 75005 Paris and UMR de Génétique Végétale, INRA/Univ. Paris-Sud/CNRS, 91190 Gif-sur-Yvette, France.
authors.forename: Celine
authors.initials: C
authors.lastname: Lévy-Leduc
authors.affiliation: AgroParisTech/INRA MIA 518, 75005 Paris and UMR de Génétique Végétale, INRA/Univ. Paris-Sud/CNRS, 91190 Gif-sur-Yvette, France.
authors.forename: M
authors.initials: M
authors.lastname: Delattre
authors.affiliation: AgroParisTech/INRA MIA 518, 75005 Paris and UMR de Génétique Végétale, INRA/Univ. Paris-Sud/CNRS, 91190 Gif-sur-Yvette, France AgroParisTech/INRA MIA 518, 75005 Paris and UMR de Génétique Végétale, INRA/Univ. Paris-Sud/CNRS, 91190 Gif-sur-Yvette, France.
authors.forename: T
authors.initials: T
authors.lastname: Mary-Huard
authors.affiliation: AgroParisTech/INRA MIA 518, 75005 Paris and UMR de Génétique Végétale, INRA/Univ. Paris-Sud/CNRS, 91190 Gif-sur-Yvette, France.
authors.forename: S
authors.initials: S
authors.lastname: Robin
mesh_terms: D000818:Animals; D002843:Chromatin / Q000737:chemistry; D002877:Chromosomes, Human / Q000737:chemistry; D033481:Chromosomes, Mammalian / Q000737:chemistry*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D051379:Mice; D015233:Models, Statistical; D017422:Sequence Analysis, DNA
chemical_list: D002843:Chromatin