Yes, in Step 1 of 4 of the Single Experiment Analysis workflow, you can select what kinds of pathways (available for the chosen organism) are queried during Pathway Analysis depending on whether you would like to include only Curated pathways, or Literature Derived Networks, or both. You can even narrow down your selection based on the respective sources (WikiPathways, BioCyc, BioPAX, GPML, Hand created, and Legacy for Curated pathways; NLP and MeSH terms for Literature Derived Networks).