Year: 2016
Type: article
Abstract: MOTIVATION: Topological domains have been proposed as the backbone of interphase chromosome structure. They are regions of high local contact frequency separated by sharp boundaries. Genes within a domain often have correlated transcription. In this paper, we present a computational efficient spectral algorithm to identify topological domains from chromosome conformation data (Hi-C data). We consider the genome as a weighted graph with vertices defined by loci on a chromosome and the edge weights given by interaction frequency between two loci. Laplacian-based graph segmentation is then applied iteratively to obtain the domains at the given compactness level. Comparison with algorithms in the literature shows the advantage of the proposed strategy. RESULTS: An efficient algorithm is presented to identify topological domains from the Hi-C matrix. AVAILABILITY AND IMPLEMENTATION: The Matlab source code and illustrative examples are available at http://bionetworks.ccmb.med.umich.edu/ CONTACT: : [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics
Authors: Jie Chen, Alfred O. Hero, Indika Rajapakse
Institutions: Northwestern Polytechnical University, University of Michigan
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: bronze
OpenAlex ID: W2345889914