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)
PD_combined Exclusive	GWAS	7.28e-01	5.56e-01	7.52e-01	8.29e-03
GWAS Exclusive	PD_combined	3.94e-01	1.50e-01	1.86e-04	3.53e-01
PD_combined Exclusive	GWAS Exclusive	5.08e-01	5.17e-01	8.14e-01	2.31e-03
GWAS Exclusive	PD_combined Exclusive	4.88e-01	3.09e-01	3.24e-04	2.69e-01
PD_combined Exclusive	Overlap	9.97e-01	9.86e-01	9.94e-01	9.58e-01
GWAS Exclusive	Overlap	1.15e-01	1.27e-01	1.68e-01	2.22e-01
Overlap	Exclusives	1.16e-02	8.31e-02	3.94e-01	1.39e-02



Evaluating how well PD_combined 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)
PD_combined Exclusive	GWAS	0.61	0.97	1.06	0.98	3.19
GWAS Exclusive	PD_combined	0.53	1.79	1.96	1.81	1.09
PD_combined Exclusive	GWAS Exclusive	0.62	1.23	1.20	0.90	3.89
GWAS Exclusive	PD_combined Exclusive	0.52	1.83	1.37	1.52	1.39
PD_combined Exclusive	Overlap	0.46	-0.15	-0.11	0.06	-0.21
GWAS Exclusive	Overlap	0.63	1.88	1.83	1.05	1.11
Overlap	Exclusives	0.56	1.93	2.26	1.97	2.64

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)
PD_combined Exclusive	GWAS	0.01	1.44	1.23	1.12	2.86
GWAS Exclusive	PD_combined	0.01	0.87	3.15	2.07	1.52
PD_combined Exclusive	GWAS Exclusive	0.01	1.54	1.24	1.35	3.74
GWAS Exclusive	PD_combined Exclusive	0.01	0.57	1.32	0.54	0.92
PD_combined Exclusive	Overlap	0.00	-0.40	-0.24	-0.33	-0.59
GWAS Exclusive	Overlap	0.01	23.77	30.28	27.32	17.27
Overlap	Exclusives	0.02	2.51	3.52	2.48	3.07

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	 
PD_combined Exclusive	162	161	AP000781.2
GWAS Exclusive	71	70	CASC16
Overlap	6	6