A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations
Figure 3
Accuracy of artificial network recovery and expansion.
(A) Influence of inhibition on network recovery. AUC (y-axis) plotted as a function of the percent of inhibitory links (x-axis). Four replicate hybridizations were used in all simulations. Points and error bars represent means and standard deviations computed across 500 synthetically generated networks respectively. Lines in each plot represent the performance of FG-NEM (red) and uFG-NEM run on the original data (green) or on AVT data (blue) for both structure recovery (solid lines) and sign recovery (dotted lines). (B) Accuracy of FG-NEM network expansion compared to Template Matching. The percentile of an S-gene obtained from Template Matching was subtracted from the percentile of the LAR score (see Methods) assigned by FG-NEM and uFG-NEM obtained from the leave-one-out expansion test. A smoothed histogram for FG-NEM (red), uFG-NEM run on the original data (green) and the AVT data (blue) was plotted and shows the proportion of S-genes (y-axis) with a particular difference in method percentile (x-axis). The underlying simulated network had 32 S-genes, eight S-genes were used for network recovery, and twenty E-genes were attached to each S-gene.