GREAT offers both global and per-ontology export options that enable export / download of table data.
All data as .tsv
The "All data as .tsv" export offers download of a tab-delimited file that is useful for further manipulation in a spreadsheet program (like Excel) or with a scripting language. It includes all GREAT statistics (i.e. both shown and hidden columns) along with the names of the region and gene hits for each term. Like the GREAT Programming Interface Batch mode, up to 500 rows are returned per ontology.
Aside from annotation count, the export is not filtered (i.e. no p-value cutoff, minimum observed genes hit, or minimum fold enrichment filter).
The header specifies the GREAT version number, the species assembly, and the regulatory domain parameters. It also includes internal documentation explaining the data in each column.
The main data export is tab-delimited, including all GREAT statistics:
The order of data columns output in a whole genome background test is:
term name / identifier
binomial p-value (uncorrected)
binomial Bonferroni corrected p-value
binomial FDR q-value
region fold enrichment (k/(n*p))
expected region hits (n*p)
observed region hits (k)
genome fraction (p)
region set coverage (k/n)
hypergeometric p-value (uncorrected)
hypergeometric Bonferroni corrected p-value
hypergeometric FDR q-value
gene fold enrichment (k*N/(n*K))
expected gene hits (n*K/N)
observed gene hits (k)
total genes, a.k.a "annotation count" (K)
gene set coverage (k/n)
term gene coverage (k/K)
names of region hits
names of gene hits
The order of data columns output in a foreground/background test is:
term name / identifier
Bonferroni corrected p-value
region fold enrichment (k*N/(n*K))
expected foreground region hits (n*K/N)
observed foreground region hits (k)
background region hits (K)
foreground region set coverage (k/n)
term foreground coverage (k/K)
number of genes annotated with term hit by foreground regions
number of genes annotated with term hit by background regions
total number of genes in the genome annotated with the term
names of foreground regions associated with one or more genes annotated with the term
names of background regions associated with one or more genes annotated with the term
names of genes annotated with the term hit by one or more foreground regions
names of genes annotated with the term hit by one or more background regions
The footer lists the tested ontologies, the number of terms tested per ontology, and the minimum and maximum annotation counts for each ontology.
All shown data as HTML
The "All shown data as HTML" export option offers a clean, readable dump of the currently shown GREAT results for all ontologies. It is useful for preparing presentation and publication quality tables. It can be further edited with any HTML editor.
The rows and columns included in the export match those currently shown in the GREAT tables; thus, the exported results are filtered exactly like in the GREAT tables.
All shown data as TSV
The "All shown data as TSV" export offers a tab-delimited dump of the data currently shown in the GREAT tables for all ontologies. Columns are ordered as in the display. The file can be opened with most spreadsheet programs for further manipulation.
Per Ontology Export
GREAT offers a per-ontology export option with the same functionality as the global export but with results limited to a single ontology.
Use "Export > Shown ontology data as HTML" to view the displayed ontology data in a simple format optimized for reading.
Use "Export > Shown ontology data as .tsv" to download the displayed ontology data for further processing.
Use "Export > All ontology data as .tsv" to download all ontology data for further processing. This includes hidden rows and columns and the genes and regions that hit each term.