MotifMap: integrative genome-wide maps of regulatory motif sites for model species

BMC Bioinformatics

Table 3 Performance comparison of the prototype and updated MotifMap pipelines

	NFKB	MYC	P53	STAT1	CTCF	NRSE
AUC
Prototype, 17 species	0.722	0.683	0.861	0.606	0.814	0.941
Update, 17 species	0.797	0.765	0.902	0.780	0.887	0.950
Update, 32 species	0.786	0.812	0.896	0.820	0.903	0.951
Number of sites
Prototype, 17 species	11,636	55,271	28,635	6,134	69,446	13,055
Update, 17 species	13,924	100,311	24,880	9,537	53,794	7,488
Update, 32 species	14,839	100,275	25,563	10,034	77,064	8,127

Area under the ROC curve (AUC) and number of sites found for the prototype MotifMap pipeline versus the updated MotifMap pipeline (performed with the original 17-species alignment and a newer 32-species alignment); the best performing method for each motif is shown in bold.

ISSN: 1471-2105