Two-dimensional segmentation for analyzing HiC data

Archive ouverte

Levy Leduc, Celine | Delattre, Maud | Mary-Huard, Tristan | Robin, Stephane

Edité par CCSD -

Conference: 13th European Conference on Computational Biology (ECCB)Location: Strasbourg, FRANCEDate: SEP 07-10, 2014Sponsor(s):BioBase; Sbv IMPROVER; Koriscale; Totalinux; Genom, Proteom & Bioinformat. 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.

• Description
• Sujet/Public
• Outil
• Outil d'anticipation
• Mémoire et thèse
• Gestion