Evaluating tools for transcription factor binding site prediction

BMC Bioinformatics

Table 2 Performance of the different motif discovery tools using FIMO

Motif discovery tool	Sn	PPV	ACC _g	FPR _s
ChIPMunk	0.886	0.786	0.834	0.009
HOMER	0.901	0.795	0.846	0.007
MEME-ChIP	0.865	0.771	0.817	0.013
rGADEM	0.933	0.839	0.884	0.002

Average sensitivities (Sn), Positive Predictive Value (PPV), geometric accuracy (ACC _g) and false positive rate on scrambled sequences (FPR _s) are reported. The best-performing tool rGADEM is highlighted in bold. Note that TFBS PWMs were generated only for the 12 transcription factors in the PAZAR-E dataset

ISSN: 1471-2105