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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

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).

What is a UCSC Genome Browser Custom Track?

A custom track in the UCSC Genome Browser is a way of displaying one's own annotation data in the browser. GREAT can automatically open your test regions as a custom track in the UCSC Genome Browser. It can also create annotation term specific custom tracks of the regions in your test set associated with the annotation term (available on the Term Details page accessed by clicking on a term description). Custom tracks are only viewable on the machine from which they were uploaded and are discarded 48 hours after their last access. More information is available at UCSC Genome Bioinformatics.

Output Filters

GREAT offers a number of filters that affect both the display and processing of the output data:

  • Minimum binomial fold enrichment - Only display terms with a binomial fold enrichment (observed regions hit / expected regions hit) greater than or equal to this value. This filter is useful for avoiding general terms, which can achieve strong p-values with moderate fold enrichments. Fold enrichment is a measure of effect size.
  • Observed gene hits - Only display terms that hit at least this many different genes. This filter is useful for avoiding enrichments due to a number of different regions hitting the same genes repeatedly.
  • Minimum annotation count - Only display terms that are applied to at least this number of genes in the ontology.

Why are some filters absent when I run the foreground-background test?

  • The Minimum binomial fold enrichment filter does not apply when an explicit background is provided. The binomial test is only performed with a whole genome background, not with an explicit background.
  • The Minimum annotation count filter is not implemented when an explicit background is provided. We plan to provide it in a future version.

Ontology Table Controls

Each ontology table has a set of controls which operate exclusively on that table's content.

  • The Export control allows you to export that table's data.
    • Shown data as table - This brings up a new browser tab or window, with the exact data as shown in the current table, but in an HTML format that is suitable for inclusion in publications. The new page also contains the information in the footer of the table. It can be used as-is, or edited with any HTML editor.
    • Shown data as .tsv - This allows you to download a tab-separated-values file containing the exact data as shown in the current table. The file does not contain the information in the footer of the table. The file can be opened with most spreadsheet programs for further manipulation.
    • All data as .tsv - This allows you to download a tab-separated-values file containing all the data used to create the current table (i.e., all columns and rows, whether displayed or not). The file does not contain the information in the footer of the table. The file can be opened with most spreadsheet programs for further manipulation.
  • The Shown top rows in this table control allows you to choose how many rows appear in the table. If there are not enough data rows or the global table control Display is set to Summary and there are fewer of such rows than you specify in this control, then the number of rows you choose may not appear.
  • The Test min. annotation count control allows you to change the minimum annotation count used for table.
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