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The Bejerano Lab at Stanford University developed the Genomic Regions Enrichment of Annotations Tool (GREAT) and hosts the GREAT web server.

Many coding genes are well annotated with their biological functions. Non-coding regions typically lack such annotation. GREAT 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. Cis-regulatory regions can be identified via both experimental methods (e.g. chromatin immunoprecipitation followed by massively parallel sequencing) and by computational methods (e.g. sequence conservation in a given clade).




  • 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?
  • File Size - What data set sizes can GREAT handle?
  • Data Integrity - What checks does GREAT perform to ensure my data is valid?
  • Background Sets - When should I use an explicit 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?
  • Programming Interface - How can I send data sets directly to GREAT?


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