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

Table 4

Nucleotide-level identification accuracy on the first group of simulated data sets.

		PairMotifChIP			MEME-ChIP			F-motif			PairMotif+
		nCC	nSn	nSp	nCC	nSn	nSp	nCC	nSn	nSp	nCC	nSn	nSp
9	0.2	0.969	0.970	0.999	0.927	0.899	0.999	0.969	0.970	0.999	0.969	0.970	0.999
	0.5	0.947	0.949	0.998	0.849	0.762	0.999	0.947	0.949	0.998	0.947	0.949	0.998
	0.8	0.921	0.929	0.996				0.950	0.951	0.998	0.950	0.951	0.998
15	0.2	0.997	0.997	1.000	0.978	0.997	0.998	0.997	0.997	1.000	0.997	0.997	1.000
	0.5	0.983	0.984	0.999	0.952	0.950	0.997	0.983	0.984	0.999	0.983	0.984	0.999
	0.8	0.965	0.967	0.998				0.965	0.967	0.998	0.965	0.967	0.998
21	0.2	1.000	1.000	1.000	0.969	1.000	0.994	—	—	—	—	—	—
	0.5	0.993	0.994	0.999	0.972	0.955	0.996	—	—	—	—	—	—
	0.8	0.989	0.990	0.999	0.921	0.906	0.996	—	—	—	—	—	—

Note. —: the result is not obtained because the running time is over 24 hours; the result is not obtained because motif sites are not provided by MEME-ChIP on the corresponding data sets. Since qPMS9 and F-motif report the same motifs and have the same identification accuracy, the results of qPMS9 are not listed in this table. Besides the nucleotide-level identification accuracy nCC, the sensitivity nSn and specificity nSp are also listed in this table.