Gene Ontology (GO) is a dynamic, structured, precisely defined, controlled vocabulary used to describe the roles of genes and gene products along with their hierarchical structure in any organism.
There are two major components to GO terms:
Although the key objective of GO project is to unify the representation of genes and gene product attributes across the species gene ontologies are particularly useful to identify enriched GO terms based on the DEGs using enrichment analysis.
Since ontologies have a hierarchical relationships, it is important to apply appropriate correction factors to minimize errors. For instance, Using a False Discovery Rate (FDR) or Family-wise Error Rate correction factor may not be appropriate for GO analysis. Advanced pruning methods like Elim and Weight as proposed by Alexa et al (2006) are more suited for such analysis. You can lean more about different correction factors in Chapter 16 of this book.