Fig. 3 | npj Systems Biology and Applications

Fig. 3

From: On the performance of de novo pathway enrichment

Fig. 3

Average performance for over 80 FG sets of size 20 nodes generated using the AVD k algorithm. Expression profiles were simulated with VM. The HPRD network was used as the input network. Performance was assessed with the F-measure for a range of internal parameter settings for each tool, i.e. the expected pathway size (M) for GXNA, the number of allowed exceptions (outliers) in a pathways (L) for KPM, and the pathway false discovery rate (FDR) for BioNet

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