Background operations

Over-representation analysis

Over-representation analysis is a statistical (hypergeometric distribution) test that determines whether certain Reactome pathways are over-represented (enriched) in the submitted data. It answers the question ‘Does my list contain more proteins for pathway X than would be expected by chance?’ This test produces a probability score, which is corrected for false discovery rate using the Benjamani-Hochberg method. 

Topology analysis

Pathway topology analysis considers the connectivity between molecules, which is represented by the pathway steps (known as reactions in Reactome) in the pathway. It groups all the molecules represented in each reaction as a pathway ‘unit’. If any of these molecules is represented in your query set, this is considered a match to that reaction. This may give a better indication of the proportion of the pathway that matches your data.