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) All Excluding Young (PITT,MIA, KGAD, STEP)_z_2_9_eqtls Exclusive TIER1_GS 1.57e-07 2.11e-07 2.57e-09 1.63e-09 TIER1_GS Exclusive All Excluding Young (PITT,MIA, KGAD, STEP)_z_2_9_eqtls 1.29e-01 1.74e-01 1.07e-01 2.63e-02 All Excluding Young (PITT,MIA, KGAD, STEP)_z_2_9_eqtls Exclusive TIER1_GS Exclusive 3.01e-08 1.72e-07 3.28e-09 6.11e-09 TIER1_GS Exclusive All Excluding Young (PITT,MIA, KGAD, STEP)_z_2_9_eqtls Exclusive 2.64e-01 2.47e-01 1.54e-01 2.69e-02 All Excluding Young (PITT,MIA, KGAD, STEP)_z_2_9_eqtls Exclusive Overlap 5.17e-01 5.17e-01 4.78e-01 1.86e-01 TIER1_GS Exclusive Overlap 9.85e-05 9.85e-05 2.96e-04 2.96e-04 Overlap Exclusives 1.00e-03 1.55e-04 1.64e-22 5.85e-07 Evaluating how well All Excluding Young (PITT,MIA, KGAD, STEP)_z_2_9_eqtls genes are linked to TIER1_GS 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) All Excluding Young (PITT,MIA, KGAD, STEP)_z_2_9_eqtls Exclusive TIER1_GS 0.83 5.00 5.06 4.17 7.08 TIER1_GS Exclusive All Excluding Young (PITT,MIA, KGAD, STEP)_z_2_9_eqtls 0.59 1.96 1.98 1.89 3.30 All Excluding Young (PITT,MIA, KGAD, STEP)_z_2_9_eqtls Exclusive TIER1_GS Exclusive 0.83 4.80 5.58 3.81 6.14 TIER1_GS Exclusive All Excluding Young (PITT,MIA, KGAD, STEP)_z_2_9_eqtls Exclusive 0.58 1.81 1.55 1.66 2.66 All Excluding Young (PITT,MIA, KGAD, STEP)_z_2_9_eqtls Exclusive Overlap 0.88 1.31 1.04 1.35 1.49 TIER1_GS Exclusive Overlap 1.00 2.44 1.66 2.35 2.74 Overlap Exclusives 0.65 4.46 5.00 2.61 6.22 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) All Excluding Young (PITT,MIA, KGAD, STEP)_z_2_9_eqtls Exclusive TIER1_GS 0.03 40.92 33.21 28.12 67.43 TIER1_GS Exclusive All Excluding Young (PITT,MIA, KGAD, STEP)_z_2_9_eqtls 0.01 10.66 15.35 8.38 6.64 All Excluding Young (PITT,MIA, KGAD, STEP)_z_2_9_eqtls Exclusive TIER1_GS Exclusive 0.02 41.46 35.01 28.98 20.17 TIER1_GS Exclusive All Excluding Young (PITT,MIA, KGAD, STEP)_z_2_9_eqtls Exclusive 0.01 7.84 10.55 4.44 4.24 All Excluding Young (PITT,MIA, KGAD, STEP)_z_2_9_eqtls Exclusive Overlap 0.03 41.64 94.93 52.86 0.39 TIER1_GS Exclusive Overlap 0.02 21.34 38.12 21.81 33.39 Overlap Exclusives 0.02 18.53 19.90 8.79 21.99 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 All Excluding Young (PITT,MIA, KGAD, STEP)_z_2_9_eqtls Exclusive 110 109 CLEC20A TIER1_GS Exclusive 29 28 MS4A Overlap 2 2