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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

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
  • 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. 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

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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