Mapping the semi-nested community structure of 3D chromosome contact networks
Fig 3
Cross-scale community organization in chromosome 10.
(a) Circular tree showing how domains (filled circles on the outer rim) merge into larger and larger 3D structures (filled circles on the inner rings). Each ring represents one value of GenLouvain’s resolution parameter γ, and the diameters of the filled circles are associated with their DNA length (measured by the number of Hi-C bins). The red circles mark delocalized 3D structures forming a single 3D community at γ = 0.9 (denoted 100.9). The dark links show folding trajectories for the domains passing through 100.9 towards the root. The left panel shows a two-domain folding path and defines our label convention. We plotted the tree using RAW Graphs [37]. (b) Joining and splitting of the 13 domains belonging to the community 100.9. These domains (filled dark-blue circles) pass through the 3D communities (open circles), joining other domains (filled light-blue circles). The edges connect 3D communities with dark-blue domains. We also highlighted these folding pathways in (a) (dark links).