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What do the output columns mean?

General

  • ID: Term identifier from the ontology

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
  • Fold Enrichment (kN/(nK)): fold enrichment of number of genes in the test set with the annotation (observed / expected)
  • 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
  • Term Coverage (k/K): fraction of all genes with the annotation that are tagged by the test set

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
  • Fold Enrichment (k/(np)): fold enrichment of number of genomic regions in the test set with the annotation (observed / expected)
  • 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 domain of attraction of a gene with the annotation

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).

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