What is GREAT?
Many coding genes are well annotated with their biological functions. Non-coding regions typically lack such annotation. GREAT, the Genomic Regions Enrichment of Annotations Tool, assigns biological meaning to a set of non-coding genomic regions by analyzing the annotations of the nearby genes.
When is GREAT useful?
GREAT infers biological meaning for a set of non-coding genomic regions. It is useful in studying cis functions, as it associates the input regions with the neighboring genes and infers the function of the regions from the known functions of the genes.
Many experimental and computational screens produce sets of interest for GREAT. One natural application is analyzing data from a chromatin immunoprecipitation (ChIP) experiment with a transcription factor of interest. To hypothesize the processes that involve a given transcription factor:
- Identify transcription factor binding sites via ChIP.
- Use GREAT to find annotations enriched among the genes near the binding sites.
- Hypothesize that the transcription factor helps regulate the processes whose annotations are highly enriched.
Using the GREAT web server, you can determine annotation enrichments for your regions of interest.