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)
GeneGroup1 Exclusive	GeneGroup2	7.33e-04	1.76e-05	1.51e-06	1.03e-04
GeneGroup2 Exclusive	GeneGroup1	4.63e-13	2.91e-02	8.93e-03	1.23e-02
GeneGroup1 Exclusive	GeneGroup2 Exclusive	6.51e-04	5.24e-05	8.65e-06	1.15e-04
GeneGroup2 Exclusive	GeneGroup1 Exclusive	4.26e-14	1.85e-02	3.93e-02	4.01e-03
GeneGroup1 Exclusive	Overlap	9.50e-01	7.41e-01	9.09e-01	7.84e-01
GeneGroup2 Exclusive	Overlap	1.69e-04	1.69e-04	1.69e-04	1.95e-04
Overlap	Exclusives	6.48e-17	2.33e-14	1.49e-32	2.46e-24



Evaluating how well GeneGroup1 genes are linked to GeneGroup2 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)
GeneGroup1 Exclusive	GeneGroup2	0.58	-1.67	-5.33	-2.50	3.65
GeneGroup2 Exclusive	GeneGroup1	0.46	-3.93	-2.12	-2.00	-2.15
GeneGroup1 Exclusive	GeneGroup2 Exclusive	0.58	-1.75	-5.19	-2.05	3.35
GeneGroup2 Exclusive	GeneGroup1 Exclusive	0.44	-4.23	-2.65	-2.38	-2.64
GeneGroup1 Exclusive	Overlap	0.55	-0.52	-1.28	-0.57	0.45
GeneGroup2 Exclusive	Overlap	1.00	3.78	3.52	3.07	3.76
Overlap	Exclusives	0.67	4.12	9.39	3.38	11.91

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)
GeneGroup1 Exclusive	GeneGroup2	0.01	-1.71	-4.42	-1.97	0.90
GeneGroup2 Exclusive	GeneGroup1	0.01	4.70	1.53	1.54	2.35
GeneGroup1 Exclusive	GeneGroup2 Exclusive	0.01	-1.78	-4.34	-1.68	0.64
GeneGroup2 Exclusive	GeneGroup1 Exclusive	0.01	-3.26	-1.21	-1.68	-1.48
GeneGroup1 Exclusive	Overlap	0.00	-0.48	-1.02	-0.54	-0.21
GeneGroup2 Exclusive	Overlap	0.11	313.82	469.82	425.77	317.97
Overlap	Exclusives	0.10	46.75	80.62	28.45	82.15

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	 
GeneGroup1 Exclusive	171	168	UBE2NL;C17orf66;LSMD1
GeneGroup2 Exclusive	208	152	MIR8061;MIR10B;MIR1301;MIR483;MIR409;MIR181C;MIR222;MIR6803;COX2;MIR200A;MIR214;MIR335;MIR885;MIR628;MIR4482;MIR2116;MIR7704;MIR432;MIR1908;MIR27A;MIR127;MIR744;MIR3173;MIR6741;MIR144;MIR377;MIR487B;MIR1260B;MIR151A;MIRLET7D;FAM234A;MIR4516;CBS;MIR141;MIR939;MIR375;MIR203A;MIR30A;MIR1226;MIR1228;MIR221;MIR1260A;MIR1307;MIR92B;MIR339;MIR33B;MIR1296;ND1;MIR17HG;MIR204;MIR98;MIR215;MIR205;MIR1306;MIR485;MIR1249
Overlap	4	4