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)
MalaCard-T2D Exclusive	HPO-T2D	2.09e-02	9.26e-03	1.92e-12	3.35e-08
HPO-T2D Exclusive	MalaCard-T2D	2.53e-02	6.02e-04	1.29e-06	1.28e-09
MalaCard-T2D Exclusive	HPO-T2D Exclusive	3.45e-01	1.43e-01	7.22e-07	3.01e-03
HPO-T2D Exclusive	MalaCard-T2D Exclusive	2.72e-01	3.39e-01	6.59e-01	9.26e-01
MalaCard-T2D Exclusive	Overlap	3.21e-17	1.17e-17	4.07e-21	1.48e-22
HPO-T2D Exclusive	Overlap	2.12e-02	2.66e-04	1.14e-07	5.45e-10
Overlap	Exclusives	2.27e-02	4.78e-02	8.15e-05	6.21e-07



Evaluating how well MalaCard-T2D genes are linked to HPO-T2D 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)
MalaCard-T2D Exclusive	HPO-T2D	0.65	0.30	0.87	0.40	6.19
HPO-T2D Exclusive	MalaCard-T2D	0.80	1.80	3.73	2.10	5.99
MalaCard-T2D Exclusive	HPO-T2D Exclusive	0.57	-0.85	-3.04	-0.71	2.46
HPO-T2D Exclusive	MalaCard-T2D Exclusive	0.50	-0.88	-1.27	-0.63	-0.02
MalaCard-T2D Exclusive	Overlap	0.97	3.34	9.55	3.13	9.49
HPO-T2D Exclusive	Overlap	0.83	1.85	4.45	2.74	6.68
Overlap	Exclusives	0.64	1.63	2.52	1.08	5.69

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)
MalaCard-T2D Exclusive	HPO-T2D	0.02	2.10	9.30	2.47	8.08
HPO-T2D Exclusive	MalaCard-T2D	0.00	0.39	2.46	1.86	0.56
MalaCard-T2D Exclusive	HPO-T2D Exclusive	0.01	-0.82	-2.24	-0.47	0.58
HPO-T2D Exclusive	MalaCard-T2D Exclusive	0.00	-0.55	-1.07	-0.32	-0.19
MalaCard-T2D Exclusive	Overlap	0.03	8.01	68.88	21.22	90.70
HPO-T2D Exclusive	Overlap	0.01	0.34	4.39	3.00	9.75
Overlap	Exclusives	0.01	2.90	3.36	2.36	9.39

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	 
MalaCard-T2D Exclusive	3	3	
HPO-T2D Exclusive	129	126	PWRN1;SNORD115-1;SNORD116-1
Overlap	29	29