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)
EA-ML Exclusive	MAGMA	7.10e-02	2.44e-01	1.85e-01	1.05e-02
MAGMA Exclusive	EA-ML	8.51e-01	6.01e-01	6.43e-03	3.80e-01
EA-ML Exclusive	MAGMA Exclusive	2.75e-01	3.06e-01	3.76e-01	9.49e-03
MAGMA Exclusive	EA-ML Exclusive	9.20e-01	9.68e-01	1.38e-02	5.78e-01
EA-ML Exclusive	Overlap	7.91e-03	6.03e-02	2.45e-02	1.61e-02
MAGMA Exclusive	Overlap	2.52e-01	1.70e-01	3.65e-02	1.40e-01
Overlap	Exclusives	1.54e-01	1.05e-02	7.76e-03	1.17e-02



Evaluating how well EA-ML genes are linked to MAGMA 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)
EA-ML Exclusive	MAGMA	0.65	2.35	1.67	2.15	3.34
MAGMA Exclusive	EA-ML	0.48	0.11	0.77	0.03	-0.77
EA-ML Exclusive	MAGMA Exclusive	0.65	0.87	0.97	0.36	2.07
MAGMA Exclusive	EA-ML Exclusive	0.46	-0.24	0.07	-0.35	-1.00
EA-ML Exclusive	Overlap	0.65	2.30	1.40	2.43	1.56
MAGMA Exclusive	Overlap	0.57	1.12	1.92	1.15	0.90
Overlap	Exclusives	0.58	2.20	3.72	2.92	2.55

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)
EA-ML Exclusive	MAGMA	0.00	3.41	0.40	2.30	0.94
MAGMA Exclusive	EA-ML	0.00	0.80	2.52	0.23	0.59
EA-ML Exclusive	MAGMA Exclusive	0.00	0.41	-0.28	-0.24	0.09
MAGMA Exclusive	EA-ML Exclusive	0.00	0.22	1.36	0.05	-0.03
EA-ML Exclusive	Overlap	0.00	3.15	0.99	0.04	3.72
MAGMA Exclusive	Overlap	0.00	1.71	1.87	0.44	0.28
Overlap	Exclusives	0.01	2.01	4.92	3.26	1.21

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	 
EA-ML Exclusive	66	66	
MAGMA Exclusive	15	15	
Overlap	13	13