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) PathwayEAML GWAS 5.84e-05 1.20e-01 6.89e-03 1.39e-01 GWAS PathwayEAML 1.44e-06 2.37e-03 9.87e-02 1.08e-03 Evaluating how well PathwayEAML genes are linked to GWAS 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) PathwayEAML GWAS 0.54 -2.26 -1.68 -1.24 0.63 GWAS PathwayEAML 0.56 -1.06 -2.87 -0.78 2.14 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) PathwayEAML GWAS 0.00 -0.98 -1.26 -0.52 -0.16 GWAS PathwayEAML 0.01 -0.94 -2.21 -0.71 0.01 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 PathwayEAML 125 124 TFDP2 GWAS 25 25