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  • 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

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View

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

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