Detecting hierarchical genome folding with network modularity.
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ABSTRACT:
SUBMITTER: Norton HK
PROVIDER: S-EPMC6029251 | biostudies-literature | 2018 Feb
REPOSITORIES: biostudies-literature
Publications
Detecting hierarchical genome folding with network modularity.
Norton Heidi K HK Emerson Daniel J DJ Huang Harvey H Kim Jesi J Titus Katelyn R KR Gu Shi S Bassett Danielle S DS Phillips-Cremins Jennifer E JE
Nature methods 20180115 2
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs and looping interactions. Here, we describe 3DNetMod, a graph theory-based method for sensitive and accurate detection of chromatin domains across length scales in Hi-C data. We identify nested, partially overlapping TADs and subTADs genome wide by optimizing network modularity and varying a single resolution parameter. 3DNetMod can be applied broadly to understand genome reconfiguratio ...[more]
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