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Note that GREAT measures all distances from the transcription start site of a gene's canonical isoform.

Approach 1

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- Basal plus extension

Each gene is assigned a basal regulatory domain of a minimum distance upstream and downstream of the TSS (regardless of other nearby genes). The gene regulatory domain is extended in both directions to the nearest gene's basal domain but no more than a maximum extension in one direction. When extending the regulatory domain of gene G beyond its basal domain, the extension to the "left" extends until it reaches the first basal domain of any gene whose transcription start site is "left" of G's transcription start site (and analogously for extending "right").

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Note: The methodology of extending beyond basal domains was slightly different in the previous GREAT v1.2 release.

Approach 2

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- Two nearest genes

Each gene is assigned a regulatory domain that extends in both directions to the nearest gene's TSS but no more than a maximum extension in one direction.

Approach 3

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- Single nearest gene

Each gene is assigned a regulatory domain that extends in both directions to the midpoint between the gene's TSS and the nearest gene's TSS but no more than a maximum extension in one direction. This has the effect of assigning a region to the single nearest gene.

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