Figure 3.

GeneEMBED candidates are significantly related to curated sets of AD genes

(A) Receiver operator characteristic curves are shown for Disc. VIS^EA for network diffusion to CTD and ClinVar AD gene sets. To determine significance of observed area under the curve (AUC), a permutation testing strategy is used wherein random gene sets of the same size are generated 100 times and analyzed through nDiffusion to create a random distribution of AUCs. Reported Z-scores are calculated relative to these backgrounds. y axis of the ROC plots are true positive rates (TPRs), and x axis is false-positive rate (FPR). Similarly, y axis of the Z score distribution is probability density, and x axis is the AUROC score of random gene sets.

(B–D) Analogous plots are shown for (B) Ext VIS^EA, (C) Disc VIS^PPh2, and (D) Ext VIS^PPh2.