Introduction

MOTIVATION: 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. AVAILABILITY AND IMPLEMENTATION: The HiCseg R package is available from the Comprehensive R Archive Network and from the Web page of the corresponding author.

Publications

  1. Two-dimensional segmentation for analyzing Hi-C data.
    Cite this
    Lévy-Leduc C, Delattre M, Mary-Huard T, Robin S, 2014-09-01 - Bioinformatics (Oxford, England)

Credits

  1. Celine Lévy-Leduc
    Developer

    AgroParisTech/INRA MIA 518, 75005 Paris and UMR de Génétique Végétale, France

  2. M Delattre
    Developer

    AgroParisTech/INRA MIA 518, 75005 Paris and UMR de Génétique Végétale, France

  3. T Mary-Huard
    Developer

    AgroParisTech/INRA MIA 518, 75005 Paris and UMR de Génétique Végétale, France

  4. S Robin
    Investigator

    AgroParisTech/INRA MIA 518, 75005 Paris and UMR de Génétique Végétale, France

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Summary
AccessionBT001572
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionFrance
Submitted ByS Robin