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The basal+extension association rule has been modified slightly in GREAT version 1.5 to handle asymmetrical basal regulatory domains in a different manner. The difference is shown in the below figure, with previous versions of GREAT generating regulatory domains as shown in (a) and GREAT version 1.5 generating regulatory domains as in (b).

In particular, note that (a) in previous GREAT versions the red gene's regulatory domain extends up to the basal domain of the blue gene (whose transcription start site is nearest) and overlaps some of the gray gene's basal domain. (b) In GREAT version 1.5, each regulatory domain extension only goes up to the nearest basal domain in each direction. Thus, the red gene's domain stops when it hits the gray gene's basal domain. Note that blue's domain still extends down to red even though the basal domain of gray overlaps it.

This logical modification only manifests itself for basal domains that are asymmetric with respect to basal extension upstream and downstream of a gene, and then only for situations like those pictured above with genes in opposite orientation near each other.

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