# What do the output columns mean?

Clicking on a column name causes that column to be displayed and all tables to be sorted by it. All *Rank* and *p-value* columns are sorted in ascending order, all others in descending order.

## General

- ID: Term identifier from the ontology

## Binomial

- Rank: ordinal rank of the p-value compared to the p-values of other annotations
- Raw p-value: uncorrected p-value from the binomial test
- Bonferroni p-Value: Bonferroni corrected p-value
- FDR q-Value: False discovery rate q-value. Note that you cannot sort the table using this column (which is why its heading is in
*italics*). - Fold Enrichment (k/(np)): fold enrichment of number of genomic regions in the test set with the annotation (observed / expected)
- where n is the number of genes in the test set

- Expected (np): expected number of genomic regions in the test set with the annotation
- Hits (k): actual number of genomic regions in the test set with the annotation
- Genome Fraction (p): fraction of bases in the genome that lie in the regulatory domain of a gene with the annotation
- Set Coverage (k/n): the fraction of all genomic regions in the test set that lie in the regulatory domain of a gene with the annotation

## Hypergeometric

- Rank: ordinal rank of the p-value compared to the p-values of other annotations
- Raw p-value: uncorrected p-value from the hypergeometric test
- Bonferroni p-value: Bonferroni corrected p-value
- FDR q-value: False discovery rate q-value. Note that you cannot sort the table using this column (which is why its heading is in
*italics*). - Fold Enrichment (kN/(nK)): fold enrichment of number of genes in the test set with the annotation (observed / expected)
- where N is the number of genes in the genome
- and n is the number of genes in the test set

- Expected (nK/N): expected number of genes in the test set with the annotation
- Observed (k): actual number of genes in the test set with the annotation
- Total Genes (K): number of genes in the genome with the annotation
- Set Coverage (k/n): the fraction of all genes in the test set with the annotation
- Term Coverage (k/K): fraction of all genes with the annotation that are tagged by the test set

# Display

GREAT's initial output display shows a summary view of only the information statistically significant by both the binomial and hypergeometric tests. Switching the *Display* control to *Full* reveals all test results (including those that are not statistically significant by one or both tests).