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)
dpp Exclusive	ctd	1.14e-02	6.21e-02	3.44e-20	3.85e-16
ctd Exclusive	dpp	1.02e-04	6.67e-02	2.95e-12	1.26e-09
dpp Exclusive	ctd Exclusive	2.21e-03	4.81e-02	2.29e-18	3.87e-16
ctd Exclusive	dpp Exclusive	9.34e-05	1.02e-01	1.81e-11	2.37e-09
dpp Exclusive	Overlap	2.17e-01	8.11e-01	1.33e-01	2.28e-01
ctd Exclusive	Overlap	9.92e-02	9.92e-02	9.92e-02	9.92e-02
Overlap	Exclusives	5.48e-17	8.28e-08	6.32e-54	9.44e-37



Evaluating how well dpp genes are linked to ctd 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)
dpp Exclusive	ctd	0.80	2.91	4.03	3.78	9.93
ctd Exclusive	dpp	0.70	-3.79	2.68	2.07	8.17
dpp Exclusive	ctd Exclusive	0.80	3.92	4.83	3.05	10.28
ctd Exclusive	dpp Exclusive	0.70	-3.66	2.20	1.76	9.15
dpp Exclusive	Overlap	0.85	-0.96	0.21	0.94	1.23
ctd Exclusive	Overlap	1.00	2.03	1.66	1.95	1.90
Overlap	Exclusives	0.79	2.37	7.52	2.73	14.21

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)
dpp Exclusive	ctd	0.02	2.04	2.31	9.13	32.12
ctd Exclusive	dpp	0.02	-0.53	7.96	11.63	11.38
dpp Exclusive	ctd Exclusive	0.02	2.78	2.58	8.44	8.99
ctd Exclusive	dpp Exclusive	0.02	-1.30	4.57	8.07	10.90
dpp Exclusive	Overlap	0.00	-0.62	-0.42	0.25	0.21
ctd Exclusive	Overlap	0.07	342.94	915.85	361.76	218.99
Overlap	Exclusives	0.04	5.74	16.02	3.25	44.24

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	 
dpp Exclusive	127	126	BRD2
ctd Exclusive	102	88	MIR296;MIR505;SNAR-I;CTR1B;CTR1C;MIR708;MIR124A-3;ATP7;MIR766;MIR4467;MIR100;MIR375;MIR146A;MIR3622B
Overlap	1	1