Do relations to a functional class in a pathway include known relations to the proteins contained in the functional class?

Functional classes are a recognized type of entity within Pathway Studio.  Relations to the functional class are specifically for the functional class entity itself.

Most functional classes do not contain proteins mapped to them, however a small subset of functional classes contain protein members (generally those found in the Ariadne curated pathways).  To see if any proteins have been mapped to a specific functional class, double click on the functional class entity in the pathway to open the Properties dialog and select the Members tab.  (If the Members tab is empty, the functional class contains no proteins.)

When using the build pathway tools within Pathway Studio to find relations to a specific functional class, the proteins mapped to that functional class are NOT considered.

When running “Gene Set Enrichment Analysis” (GSEA) and “Find Pathways/Groups Enriched with Selected Entities” (Fisher’s Exact Test) there is a check box (selected in the default setting) “Expand the Content of Functional Classes and Complexes in Target Gene Sets.”  This option allows for the proteins mapped to the functional classes to be included in the analysis.