Table 2.

Comparison between the results of SAlign (SA) and existing techniques on network pairs which have high percentage of proteins with experimentally resolved 3D structures on the basis of AFS and percentage of aligned nodes w.r.t MF and BP

Pairs	Evaluation criteria	SA	${\text{SA}}^{\mathrm{mc}}$	HA	MA	IBN	NET	M++	PRO
Results on HINT datasets (a)
Mouse human	AFS${}_{\mathit{MF}}$	0.58	0.55	0.48	0.42	0.35	0.33	0.36	0.58
	AFS${}_{\mathit{BP}}$	0.43	0.41	0.34	0.30	0.26	0.24	0.26	0.45
	Nodes${}_{\mathit{MF}}$	82	82	78	74	72	73	76	82
	Nodes${}_{\mathit{BP}}$	85	86	84	81	83	82	82	84
Mouse yeast	AFS${}_{\mathit{MF}}$	0.40*	0.39	0.36	0.31	0.29	0.31	0.29	0.36
	AFS${}_{\mathit{BP}}$	0.27*	0.26	0.25	0.23	0.21	0.22	0.21	0.25
	Nodes${}_{\mathit{MF}}$	72	73	71	71	63	64	67	53
	Nodes${}_{\mathit{BP}}$	92	91	90	88	76	83	83	69
Human yeast	AFS${}_{\mathit{MF}}$	0.48*	0.46	0.46	0.26	0.30	0.26	0.26	0.42
	AFS${}_{\mathit{BP}}$	0.35*	0.33	0.34	0.22	0.24	0.22	0.22	0.32
	Nodes${}_{\mathit{MF}}$	64	63	63	60	58	60	59	57
	Nodes${}_{\mathit{BP}}$	76	76	76	72	70	72	70	68
Avg.	AFS${}_{\mathit{MF}}$	0.49	0.47	0.43	0.33	0.31	0.30	0.31	0.45
	AFS${}_{\mathit{BP}}$	0.35	0.33	0.31	0.25	0.24	0.23	0.24	0.34
	Nodes${}_{\mathit{MF}}$	73	73	71	68	64	66	67	64
	Nodes${}_{\mathit{BP}}$	84	84	83	80	76	79	78	74
Results on BioGRID datasets (b)
Mouse human	AFS${}_{\mathit{MF}}$	0.64	0.63	0.57	0.46	0.35	0.33	0.36	0.63
	AFS${}_{\mathit{BP}}$	0.48	0.47	0.43	0.35	0.27	0.26	0.28	0.48
	Nodes${}_{\mathit{MF}}$	89	89	88	85	80	83	86	83
	Nodes${}_{\mathit{BP}}$	96	96	95	93	90	93	96	93
Mouse yeast	AFS${}_{\mathit{MF}}$	0.47	0.46	0.44	0.37	0.28	0.27	0.33	0.47
	AFS${}_{\mathit{BP}}$	0.32	0.32	0.29	0.27	0.22	0.22	0.22	0.32
	Nodes${}_{\mathit{MF}}$	82	82	80	80	76	77	80	58
	Nodes${}_{\mathit{BP}}$	96	96	94	97	88	92	97	67
Human yeast	AFS${}_{\mathit{MF}}$	0.53*	0.52	0.48	0.42	0.34	0.28	0.29	0.49
	AFS${}_{\mathit{BP}}$	0.39*	0.38	0.35	0.33	0.27	0.23	0.24	0.38
	Nodes${}_{\mathit{MF}}$	74	74	73	74	63	72	70	67
	Nodes${}_{\mathit{BP}}$	91	91	91	91	77	91	90	82
Avg.	AFS${}_{\mathit{MF}}$	0.55	0.54	0.50	0.42	0.32	0.29	0.33	0.53
	AFS${}_{\mathit{BP}}$	0.40	0.39	0.36	0.32	0.25	0.24	0.25	0.39
	Nodes${}_{\mathit{MF}}$	82	82	80	80	73	77	79	69
	Nodes${}_{\mathit{BP}}$	94	94	93	94	85	92	94	79

The particular results of the best aligners are differentiated from other aligners by italic text

For HINT datasets, the average AFS of SAlign w.r.t. MF and BP is 0.49 and 0.35 respectively

SAlign on average aligns 73% and 84% node in MF and BP respectively. SAlign outperforms all other aligners on the given evaluation criteria. For BioGRID datasets, the average AFS w.r.t. MF and BP is 0.53 and 0.38 respectively. SAlign on average aligns 81% and 94% node in MF and BP respectively. ‘*’ shows that the results are statistically significant