Table 2.

Comparison between methods.

A
Method	Clover			ModuleSearcher(A*)			ModuleDigger
Running time	1.6 min			0.5 min			10 s
	NM	SRR	Sn	NM	SRR	Sn	NM	SRR	Sn
OCT4, SOX2, NANOG	0	0	0	2.4	10	1.1%	6	10	27.6%
OCT4, SOX2	3.9	10	45.3%	0	0	0	2	10	49.1%
OCT4, NANOG	0	0	0	0	0	0	3	10	42.2%
SOX2, NANOG	0	0	0	2.4	10	0.9%	9	10	28.4%
B
Method	Clover			ModuleSearcher (A*)			ModuleDigger
Running time	4 min			0.5 min			20 s
	NM	SRR	Sn	NM	SRR	Sn	NM	SRR	Sn
OCT4, SOX2, NANOG	0	0	0	0	0	0	5	10	28%
OCT4, SOX2	6.8	10	45.3%	21	5	2.8%	18	10	49%
OCT4, NANOG	0	0	0	0	0	0	23	10	42%
SOX2, NANOG	0	0	0	21	4	0.5%	20	10	9%

(A) For all algorithms we used as input the benchmark set, the PWMs of OCT4, SOX2, NANOG and one random PWM. NM: number of modules present in the output for those runs where the RR = 1 (average over runs where RR = 1). SRR (summation of recovery rate): number of runs for which the output contained a module corresponding to the valid modules (OCT4, SOX2, NANOG or combinations thereof). Sn: number of genes containing the valid module in the output (average of runs for which RR was 1). (B) Similar to (A) but using OCT4, SOX2, NANOG in combination with 7 randomly selected PWMs.