Fig. 1

The process of evaluating a pathway analysis method based on their ability to identify target pathways. Each pathway analysis method is applied on 75 data sets. Methods are evaluated based on their ability to rank the target pathways. In this example, a data set of Alzheimer’s disease is examined, and thus, the target pathway is “Alzheimer’s disease.” Each method produces lists of ranks and p values of the target pathways, which are then used to assess its performance