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)
Reactome-AC4 Exclusive	BRCA-All-GS	5.78e-08	2.33e-05	2.46e-14	1.44e-16
BRCA-All-GS Exclusive	Reactome-AC4	2.67e-07	6.70e-04	3.55e-24	1.36e-09
Reactome-AC4 Exclusive	BRCA-All-GS Exclusive	2.17e-06	3.07e-02	4.75e-09	1.47e-11
BRCA-All-GS Exclusive	Reactome-AC4 Exclusive	5.14e-05	5.09e-02	2.63e-20	4.55e-06
Reactome-AC4 Exclusive	Overlap	2.92e-15	3.51e-12	3.70e-16	1.44e-15
BRCA-All-GS Exclusive	Overlap	5.20e-10	2.43e-09	1.50e-15	5.67e-15
Overlap	Exclusives	3.38e-19	1.38e-11	3.01e-38	8.49e-30



Evaluating how well Reactome-AC4 genes are linked to BRCA-All-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)
Reactome-AC4 Exclusive	BRCA-All-GS	0.68	0.41	3.34	1.62	9.30
BRCA-All-GS Exclusive	Reactome-AC4	0.63	1.80	2.03	1.65	8.79
Reactome-AC4 Exclusive	BRCA-All-GS Exclusive	0.66	-0.86	2.21	0.86	7.86
BRCA-All-GS Exclusive	Reactome-AC4 Exclusive	0.61	1.62	1.17	1.36	7.00
Reactome-AC4 Exclusive	Overlap	0.96	3.26	5.71	3.13	7.46
BRCA-All-GS Exclusive	Overlap	0.98	3.50	5.91	3.38	7.15
Overlap	Exclusives	0.68	1.83	7.76	3.52	17.87

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)
Reactome-AC4 Exclusive	BRCA-All-GS	0.04	-0.85	15.55	2.96	30.56
BRCA-All-GS Exclusive	Reactome-AC4	0.06	9.17	29.92	16.15	50.01
Reactome-AC4 Exclusive	BRCA-All-GS Exclusive	0.03	-2.44	5.77	0.24	11.52
BRCA-All-GS Exclusive	Reactome-AC4 Exclusive	0.03	3.90	7.58	4.77	15.76
Reactome-AC4 Exclusive	Overlap	0.07	1.23	71.51	6.59	164.42
BRCA-All-GS Exclusive	Overlap	0.34	13.38	164.15	71.47	854.58
Overlap	Exclusives	0.12	12.94	55.25	28.54	90.69

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	 
Reactome-AC4 Exclusive	320	319	
BRCA-All-GS Exclusive	241	241	
Overlap	21	21