Procedure to check subset coverage

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Revision as of 05:51, 15 March 2024 by Pascale (talk | contribs)
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  1.  Checking maximum GO annotation coverage
    • Go to QuickGO, click on View Annotations
    • On the drop down menus at the top of the page, add filters as appropriate:
      • Taxon(s) or taxonomic range (it is possible to select for example NBCITaxon:2 for all bacteria)
      • Gene Products: it is usually desirable to select only Reviewed entry and Reference proteomes (either "Gene centric, canonical", or "Gene centric, other isoforms")
    1. On the results page listing annotations, click on the Statistics tab
      • The Summary tab shows the total number of annotations and of gene products annotated.
      • The Aspect tab shows the number of gene products annotated by GO aspect. This is the maximum coverage possible by aspect.
  2. Checking GO annotation coverage for the subset
    • Go to QuickGO, click on Explore Biology
    • Under Select Terms, slick on the Tab "Input your own"
    • Enter the list of terms in your draft subset by GO ID. This should be done on an aspect-by-aspect basis to avoid effects of inter-ontology links.
    • In the Additional Options, it is possible to select a species or a taxonomic range, if appropriate. Note the the results will be calculated faster for smaller sets of genes.
    1. Repeat the same steps as in 1.2 to get the number of genes annotated with the subset. Compare the results to see if the coverage of the subset is acceptable; otherwise edit the list of GO terms and redo the analysis.


Review Status

Last reviewed: March 15, 2024

Reviewed by Pascale Gaudet


Back to: Editing the Ontology