Overview Demo Video How to Cite Download Help Forum Bejerano Lab, Stanford University
version 1.8.2		Genomic Regions Enrichment of Annotations Tool (v1.8.2) GREAT version 4.0.4     current (08/19/2019 to now) GREAT version 3.0.0     reproduce results from 2/15/2015 to 08/18/2019) GREAT version 2.0.2     reproduce results from 4/03/2012 to 02/14/2015) GREAT version 1.8.2     reproduce results from 11/19/2010 to 04/02/2012) GREAT version 1.2.6     reproduce results from 05/20/2010 to 11/18/2010

GREAT predicts functions of cis-regulatory regions.

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).

Input choices

Species assembly	Human: GRCh37 (UCSC hg19, Feb/2009)
	Human: NCBI build 36.1 (UCSC hg18, Mar/2006)
	Mouse: NCBI build 37 (UCSC mm9, Jul/2007)
	Zebrafish: Wellcome Trust Zv9 (danRer7, Apr/2010)
	Can I use a different species or assembly?
Test regions	BED file:
	BED data:
	What should my test regions file contain?
	How can I create a test set from a UCSC Genome Browser annotation track?
Background regions	Whole genome
	BED file:
	BED data:
	When should I use a background set?
	What should my background regions file contain?

Association rule settings

Show settings

Associating genomic regions with genes

GREAT calculates statistics by associating genomic regions with nearby genes and applying the gene annotations to the regions. Association is a two step process. First, every gene is assigned a regulatory domain. Then, each genomic region is associated with all genes whose regulatory domain it overlaps.

Note that all distances are measured from the transcription start site of the gene's canonical isoform.

Basal plus extension	Proximal:  kb upstream,  kb downstream, plus Distal: up to  kb
	Gene regulatory domain definition: Each gene is assigned a basal regulatory domain of a minimum distance upstream and downstream of the TSS (regardless of other nearby genes). The gene regulatory domain is extended in both directions to the nearest gene's basal domain but no more than the maximum extension in one direction.
Two nearest genes	within kb
	Gene regulatory domain definition: Each gene is assigned a regulatory domain that extends in both directions to the nearest gene's TSS but no more than the maximum extension in one direction.
Single nearest gene	within kb
	Gene regulatory domain definition: Each gene is assigned a regulatory domain that extends in both directions to the midpoint between the gene's TSS and the nearest gene's TSS but no more than the maximum extension in one direction.
Include curated regulatory domains       What are curated regulatory domains?

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