Export

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Last updated: Jun 15, 2012 by Erich WeilerVersion comment

Overview

GREAT offers both global and per-ontology export options that enable export / download of table data.

Global Export

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.

  • The current minimum and maximum annotation counts are used to calculate corrected p-values in the export.
  • Aside from annotation count, the export is not filtered (i.e. no p-value cutoff, minimum observed genes hit, or minimum fold enrichment filter).

Header

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.

Data

The main data export is tab-delimited, including all GREAT statistics:

The order of data columns output in a whole genome background test is:

  1. ontology name
  2. term name / identifier
  3. term description
  4. binomial rank
  5. binomial p-value (uncorrected)
  6. binomial Bonferroni corrected p-value
  7. binomial FDR q-value
  8. region fold enrichment (k/(n*p))
  9. expected region hits (n*p)
  10. observed region hits (k)
  11. genome fraction (p)
  12. region set coverage (k/n)
  13. hypergeometric rank
  14. hypergeometric p-value (uncorrected)
  15. hypergeometric Bonferroni corrected p-value
  16. hypergeometric FDR q-value
  17. gene fold enrichment (k*N/(n*K))
  18. expected gene hits (n*K/N)
  19. observed gene hits (k)
  20. total genes, a.k.a "annotation count" (K)
  21. gene set coverage (k/n)
  22. term gene coverage (k/K)
  23. names of region hits
  24. names of gene hits

The order of data columns output in a foreground/background test is:

  1. ontology name
  2. term name / identifier
  3. term description
  4. rank
  5. p-value (uncorrected)
  6. Bonferroni corrected p-value
  7. FDR q-value
  8. region fold enrichment (k*N/(n*K))
  9. expected foreground region hits (n*K/N)
  10. observed foreground region hits (k)
  11. background region hits (K)
  12. foreground region set coverage (k/n)
  13. term foreground coverage (k/K)
  14. number of genes annotated with term hit by foreground regions
  15. number of genes annotated with term hit by background regions
  16. total number of genes in the genome annotated with the term
  17. names of foreground regions associated with one or more genes annotated with the term
  18. names of background regions associated with one or more genes annotated with the term
  19. names of genes annotated with the term hit by one or more foreground regions
  20. 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.