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How can I create a test set from a UCSC Genome Browser annotation track?

The UCSC Table Browser

Footnote Macro

Karolchik D. et al. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6.

provides  (1) provides a direct interface to submit data to GREAT. The submission works for any type of BED data. So, you can use the Table Browser to identify regions of interest in the genome, and then easily and directly use GREAT to examine the functional annotation enrichments of these regions.

Alternatively, the Table Browser also provides an interface for exporting an annotation track or a combination of annotation tracks to a file. One option for the output format is "BED - Browser Extensible Data", the input format used by GREAT. For example, you can export the most conserved of the non-coding regions in the genome to BED format with the Table Browser (protocol explained in

Footnote Macro

Bejerano, et al. Computational screening of conserved genomic DNA in search of functional noncoding elements. Nat. Methods. 2005 Jul;2(7):535-45.

(2)), then pass the BED file as input to GREAT to see the biological roles of the conserved regions.

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The ability to restrict the background to a subset of the entire genome is currently unsupported by GREAT. This would be necessary, for example, if your assay only studied chromosome 21--you would want to restrict enrichment analyses only to that chromosome. This could be applied on a chromosome-wide scale in future implementations of GREAT but generalization to arbitrary background sets is not completely well-defined in its modifications of gene regulatory domains, and consequently GREAT does not support this functionality in its current implementation.

References

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reference1
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Karolchik D. et al. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6.
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reference2
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Bejerano, et al. Computational screening of conserved genomic DNA in search of functional noncoding elements. Nat. Methods. 2005 Jul;2(7):535-45.