A complex network framework for unbiased statistical analyses of DNA-DNA contact maps.

ABSTRACT: Experimental techniques for the investigation of three-dimensional (3D) genome organization are being developed at a fast pace. Currently, the associated computational methods are mostly specific to the individual experimental approach. Here we present a general statistical framework that is widely applicable to the analysis of genomic contact maps, irrespective of the data acquisition and normalization processes. Within this framework DNA-DNA contact data are represented as a complex network, for which a broad number of directly applicable methods already exist. In such a network representation, DNA segments and contacts between them are denoted as nodes and edges, respectively. Furthermore, we present a robust method for generating randomized contact networks that explicitly take into ac

SUBMITTER: Kruse K 

PROVIDER: S-EPMC3553935 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature