Table 6. Results of best clustering metrics (with CYC2008 and CORUM references) obtained with DAPG (with complexes of minimum size 3) using different node ordering algorithms and applying sorting (ϕ function) in large PPIs.

Network	Node ordering	Sorting	Complexes	FMeasure	Acc	MMR
DIP-yeast	First	FREQUENCY	1,217	0.4000	0.5520	0.3615
		ID	1,141	0.3942	0.5416	0.3815
	Lexicographic	FREQUENCY	1,199	0.3872	0.5355	0.3550
		ID	1,085	0.4085	0.5565	0.3610
	Random	FREQUENCY	1,142	0.4070	0.5364	0.3491
		ID	909	0.3438	0.4808	0.2535
	Degree	FREQUENCY	1,212	0.3961	0.5489	0.3682
		ID	1,165	0.3835	0.5393	0.3560
	BFS	FREQUENCY	1,253	0.4197	0.5674	0.3751
		ID	1,242	0.3622	0.5551	0.3718
	DFS	FREQUENCY	1,210	0.4110	0.5450	0.3671
		ID	1,925	0.3830	0.5486	0.4447
Biogrid-yeast	First	FREQUENCY	5,025	0.1551	0.5691	0.3534
		ID	4,945	0.1444	0.5693	0.3371
	Lexicographic	FREQUENCY	4,999	0.1561	0.5727	0.3687
		ID	4,991	0.1740	0.5967	0.3845
	Random	FREQUENCY	5,017	0.1548	0.5718	0.3599
		ID	5,167	0.1108	0.5368	0.2614
	Degree	FREQUENCY	5,049	0.1533	0.5667	0.3439
		ID	5,004	0.1465	0.5677	0.3432
	BFS	FREQUENCY	4,977	0.1584	0.5741	0.3650
		ID	5,254	0.1047	0.5355	0.2711
	DFS	FREQUENCY	5,009	0.1570	0.5720	0.3627
		ID	4,950	0.1446	0.5800	0.3468
HPRD	First	FREQUENCY	2,437	0.3395	0.2140	0.1713
		ID	2,442	0.3200	0.2272	0.1743
	Lexicographic	FREQUENCY	2,430	0.3528	0.2103	0.1783
		ID	2,085	0.3542	0.2099	0.1643
	Random	FREQUENCY	2,430	0.3465	0.2121	0.1688
		ID	1,977	0.3464	0.1879	0.1326
	Degree	FREQUENCY	2,449	0.3401	0.2135	0.1706
		ID	2,412	0.3354	0.2127	0.1675
	BFS	FREQUENCY	2,441	0.3584	0.2139	0.1865
		ID	2,777	0.3685	0.2119	0.2066
	DFS	FREQUENCY	2,443	0.3484	0.2105	0.1668
		ID	2,313	0.3392	0.2340	0.1862
Biogrid-human	First	FREQUENCY	7,360	0.2380	0.2924	0.2387
		ID	7,200	0.2349	0.2825	0.2372
	Lexicographic	FREQUENCY	7,394	0.2474	0.2920	0.2405
		ID	7,313	0.2507	0.2738	0.2385
	Random	FREQUENCY	7,316	0.2492	0.2907	0.2332
		ID	7,663	0.2587	0.2732	0.2227
	Degree	FREQUENCY	7,375	0.2412	0.2920	0.2418
		ID	7,352	0.2352	0.2918	0.2374
	BFS	FREQUENCY	7,152	0.2453	0.2902	0.2354
		ID	8,144	0.2204	0.2854	0.2232
	DFS	FREQUENCY	7,409	0.2527	0.2917	0.2539
		ID	6,498	0.2309	0.2877	0.2228