MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions.

ABSTRACT: Genome-wide proximity ligation based assays such as Hi-C have revealed that eukaryotic genomes are organized into structural units called topologically associating domains (TADs). From a visual examination of the chromosomal contact map, however, it is clear that the organization of the domains is not simple or obvious. Instead, TADs exhibit various length scales and, in many cases, a nested arrangement. Here, by exploiting the resemblance between TADs in a chromosomal contact map and densely connected modules in a network, we formulate TAD identification as a network optimization problem and propose an algorithm, MrTADFinder, to identify TADs from intra-chromosomal contact maps. MrTADFinder is based on the network-science concept of modularity. A key component of it is deriving an appropr

SUBMITTER: Yan KK 

PROVIDER: S-EPMC5546724 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature