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)
91 Braak genes Exclusive	AD_Tier1	3.06e-01	2.13e-01	4.89e-01	1.13e-02
AD_Tier1 Exclusive	91 Braak genes	4.18e-01	5.46e-01	1.12e-01	2.84e-01
91 Braak genes Exclusive	AD_Tier1 Exclusive	3.40e-01	3.14e-01	5.82e-01	2.48e-02
AD_Tier1 Exclusive	91 Braak genes Exclusive	6.98e-01	7.21e-01	1.50e-01	5.31e-01
91 Braak genes Exclusive	Overlap	6.10e-01	5.17e-01	8.62e-01	1.92e-01
AD_Tier1 Exclusive	Overlap	9.85e-05	9.85e-05	9.85e-05	2.96e-04
Overlap	Exclusives	1.62e-05	3.25e-05	4.12e-13	3.01e-05



Evaluating how well 91 Braak genes genes are linked to AD_Tier1 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)
91 Braak genes Exclusive	AD_Tier1	0.64	1.20	1.37	0.73	2.93
AD_Tier1 Exclusive	91 Braak genes	0.54	1.65	1.10	1.28	1.57
91 Braak genes Exclusive	AD_Tier1 Exclusive	0.63	1.16	1.42	0.59	2.39
AD_Tier1 Exclusive	91 Braak genes Exclusive	0.53	1.25	0.76	1.17	0.91
91 Braak genes Exclusive	Overlap	0.83	1.42	1.56	0.90	1.80
AD_Tier1 Exclusive	Overlap	1.00	2.20	2.20	2.22	2.47
Overlap	Exclusives	0.59	3.67	3.72	1.73	3.67

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)
91 Braak genes Exclusive	AD_Tier1	0.00	0.61	0.46	0.19	2.17
AD_Tier1 Exclusive	91 Braak genes	0.01	1.49	4.32	3.39	3.69
91 Braak genes Exclusive	AD_Tier1 Exclusive	0.00	1.12	0.26	0.13	0.53
AD_Tier1 Exclusive	91 Braak genes Exclusive	0.01	0.59	1.06	0.96	0.51
91 Braak genes Exclusive	Overlap	0.00	1.27	8.45	0.12	1.35
AD_Tier1 Exclusive	Overlap	0.05	125.41	89.27	87.61	31.00
Overlap	Exclusives	0.04	85.89	61.83	31.82	31.18

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	 
91 Braak genes Exclusive	88	88	
AD_Tier1 Exclusive	29	28	MS4A
Overlap	2	2