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. Thus, it is particularly useful in studying cis functions of sets of non-coding genomic regions, including those identified by chromatin immunoprecipitation experiment or by a computational screen, such as conservation in a given clade.
- Overview - When is GREAT useful, and for which uses should I prefer it to other annotation tools?
- Citation - How do I cite GREAT?
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- Genome Assemblies - Which genome assemblies does GREAT support, and can I use other assemblies or species?
- File Formats - What should my test regions and background regions files contain?
- Background Sets - Why should I use a background set in evaluating enrichments?
- Statistics - How does GREAT calculate enrichments, and how should I interpret my results?
- Output - What output does GREAT provide?
- Genes - Which set of genes does GREAT use, and how does GREAT determine a single transcription start site for a gene?
- Ontologies - What is an ontology, and what data do the ontologies in GREAT provide?
- Web Browsers - Which web browsers does GREAT support, and how can I make my browser work best with GREAT?