One of the main uses of the GO is to perform enrichment analysis on gene sets. For example, given a set of genes that are up-regulated under certain conditions, an enrichment analysis will find which GO terms are over-represented (or under-represented) using annotations for that gene set.
Did you know you can do GSEA with just one click? The home page widget in the GOC website connects to the analysis tool from the PANTHER Classification System, which is maintained up to date with GO annotations. In addition to the 130+ genomes in the widget, PANTHER supports another 1100+ genomes from the Reference Proteome project for users to generate GO annotations.
See our quick-help page for an overview of how to interpret results, including info on background frequency, sample frequency, and p-values.
Detailed info is available on the PANTHER site.
The PANTHER classification system is explained in great detail in Mi H et al, PMID: 23868073.
The list of supported gene IDs is available from the PANTHER website. If your organism is not supported, see our FAQs.