Fig. 2
Average performance for over 80 FG sets of size 20 nodes were generated, using the AVD k algorithm, with varying signal strength (a, b) and varying sparsity (c, d). Expression profiles were simulated with varying mean (VM) (a, c) and varying variation (VV) (b, d). The HPRD network was used as the input network and the performance was assessed using the F-measure. The error-bars (a, b) and box plots (c, d) represent performance over several FG nodes and over a range of internal parameter settings for each tool. The higher the signal strength, the more different are the expression profiles of the FG vs. BG genes, indicating that we can expect pathway enrichment methods to identify them more easily. For details on internal parameters, signal strength and sparsity values, please refer to Supplementary Tables 1, 3, 5 respectively
