Comparing distributions of experimental and random diffusion values (p-values for KS tests) Seeds Recipients Randomize Seeds (degree-matched) Randomize Recipients (degree-matched) Randomize Seeds (uniform) Randomize Recipients (uniform) COMBINED 35 Exclusive AD 1.38e-05 2.04e-07 1.07e-07 2.84e-10 AD Exclusive COMBINED 35 2.80e-02 1.26e-01 2.03e-04 1.86e-02 COMBINED 35 Exclusive AD Exclusive 6.28e-04 6.98e-05 2.77e-05 7.48e-07 AD Exclusive COMBINED 35 Exclusive 2.09e-01 2.91e-01 4.81e-04 3.51e-02 COMBINED 35 Exclusive Overlap 1.05e-03 2.75e-04 3.42e-05 2.92e-04 AD Exclusive Overlap 7.45e-12 4.47e-11 4.47e-11 1.88e-09 Overlap Exclusives 7.30e-03 1.81e-02 9.56e-04 1.31e-03 Evaluating how well COMBINED 35 genes are linked to AD genes, comparing against random ROC results Seeds Recipients AUROC Z-score for Random Seeds (degree-matched) Z-score for Random Recipients (degree-matched) Z-score for Random Seeds (uniform) Z-score for Random Recipients (uniform) COMBINED 35 Exclusive AD 0.85 3.33 5.69 3.48 5.93 AD Exclusive COMBINED 35 0.58 3.63 2.57 2.14 3.49 COMBINED 35 Exclusive AD Exclusive 0.82 2.93 4.59 3.42 4.90 AD Exclusive COMBINED 35 Exclusive 0.57 2.80 1.69 1.94 2.86 COMBINED 35 Exclusive Overlap 0.95 2.98 3.28 3.12 3.04 AD Exclusive Overlap 1.00 3.40 3.31 2.90 3.60 Overlap Exclusives 0.60 2.24 4.32 2.62 4.56 PRC results Seeds Recipients AUPRC Z-score for Random Seeds (degree-matched) Z-score for Random Recipients (degree-matched) Z-score for Random Seeds (uniform) Z-score for Random Recipients (uniform) COMBINED 35 Exclusive AD 0.01 8.64 20.82 9.91 16.65 AD Exclusive COMBINED 35 0.02 23.23 20.61 13.26 21.22 COMBINED 35 Exclusive AD Exclusive 0.01 7.99 17.35 7.62 10.42 AD Exclusive COMBINED 35 Exclusive 0.01 6.64 4.97 3.41 3.83 COMBINED 35 Exclusive Overlap 0.00 3.05 3.48 13.73 0.55 AD Exclusive Overlap 0.13 271.33 582.78 247.34 464.71 Overlap Exclusives 0.05 25.99 55.38 49.14 49.16 Z-scores are computed for the experimental area under ROC or PRC based on distributions of the random areas under these curves Seeds: Genes where diffusion signal starts FROM) Recipients: Genes that receive the diffusion signal and that are in the other validated group Random genes are selected either uniformly or degree matched Number of genes ** #Total # Mapped in the network Not mapped genes COMBINED 35 Exclusive 142 140 RFPL2;AC131097.2 AD Exclusive 20 20 Overlap 5 5