What does “Expand the content of functional classes and complexes in target gene sets” in the Fisher’s Exact Test and Gene Set Enrichment Analysis mean?

In both analyses: Find Pathways/Groups Enriched with Entities (the Fisher’s Exact Test) and Gene Set Enrichment Analysis, the algorithms identify when the genes in groups or pathways are enriched in the experimental dataset.

Functional classes and complexes are entities that may have multiple proteins mapped to them (note that these entities may also be “empty” in which case no proteins are mapped to them).   When the box “Expand the content of functional classes and complexes in target gene sets “ is checked, the proteins contained in these entities are considered when the statistical significance of the enrichment is calculated.   If the box is not checked, the proteins within the Functional Classes and Complexes are not considered in the enrichment analysis.