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Beginning in GREAT version 1.5, users can download the associations between each input genomic region and the gene(s) it putatively regulates according to the association rule used. This file contains a header line indicating the GREAT version, assembly, and association rule used, and then lists the associations for each input genomic region as a two column tab-delimited entry. A sample output for an input file of three genomic regions could look like the following:

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Input.1      Gene.1 (+1234), Gene.2 (+35000)


Input.2      Gene.3 (-45434)


Input.3      NONE

The first column of the output is the user-given name of the input genomic region (the "name" field of the BED). The second column contains a comma-delimited list of all genes to which the genomic region is associated and the distance (in bp) from the middle of the input genomic region to the transcription start site (TSS) of the gene (or NONE if the genomic region is not associated with any gene). The distance also has strand information: '+' indicates that the input genomic region is downstream of the TSS and '-' indicates that the input genomic region is upstream of the TSS.

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As an example, the genomic region and gene associations file given above would cause the following observed distances to be made:

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Accounting for upstream/downstream information:


< -500 kb           0 genomic regions


-500 kb to -50 kb   0 genomic regions


-50 kb to -5 kb     1 genomic region (Input.2 associated to Gene.3)


-5 kb to 0 kb       0 genomic regions


0 kb to 5 kb        1 genomic region (Input.1 associated to Gene.1)


5 kb to 50 kb       1 genomic region (Input.1 associated to Gene.2)


50 kb to 500 kb     0 genomic regions


> 500 kb            0 genomic regions

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Ignoring upstream/downstream information:


0 kb to 5 kb        1 genomic region (Input.1 associated to Gene.1)


5 kb to 50 kb       2 genomic regions (Input.1 associated to Gene.2 and Input.2 associated to Gene.3)


50 kb to 500 kb     0 genomic regions


> 500 kb            0 genomic regions

GREAT Data Visualization

Data visualization capabilities were added starting GREAT version 2.0.

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