PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets

Table 7

Results on the mESC data.

Data set	Published motif	PairMotifChIP		PairMotif+
		Time	Predicted motif	Time	Predicted motif
c-Myc		37.2 s		4106.1 s
CTCF		29.1 s		23584.3 s
Esrrb		25.6 s		7424.6 s
Klf4		29.3 s		3558.5 s
Nanog		24.3 s		1975.6 s
n-Myc		36.3 s		33962.6 s	—
Oct4		8.9 s		2608.8 s
Smad1		20.3 s		5296.1 s	—
Sox2		23.1 s		4115.2 s
STAT3		22.9 s		6342.6 s	—
Tcfcp2I1		23.5 s		2269.5 s	—
Zfx		42.2 s		3617.2 s

Note. —: there is no motif overlapping the published motif in the top ten predicted motifs.