3D structure

Topological associating domains. A self-interacting genomic region, meaning that DNA sequences within a TAD physically interact with each other more frequently than with sequences outside the TAD.

Possible relationships:

TAD -[overlap/locate_in/downstream/upstream]- (any entities with coordinates)

In a DNA looping event, chromatin forms physical loops, bringing DNA regions into close contact. Thus, even regions that are far apart along the linear chromosome can be brought together in three-dimensional space.

Since loops have two anchor locations, positional relationships “locate_in”, “upstream”, and “downstream” might be ambiguous, only “overlap” is supported in GenomicKB (i.e., an entity overlaps with loop anchors).

Possible relationships:

loop -[overlap]- (any entities with coordinates)

Frequently interacting regions(FIREs) is identified by studying a compendium of Hi-C datasets across 14 human primary tissues and 7 cell types.

Ref: https://www.sciencedirect.com/science/article/pii/S2211124716314814

Possible relationships:

FIRE_region -[overlap/locate_in/downstream/upstream]- (any entities with coordinates)

Researchers noticed that the whole genome could be split into two spatial compartments, labelled A and B, where regions in compartment A tend to interact preferentially with A compartment-associated regions than B compartment-associated ones. Similarly, regions in compartment B tend to associate with other B compartment-associated regions.

Possible relationships:

AB_compartment -[overlap/locate_in/downstream/upstream]- (any entities with coordinates)