Genome-wide prediction of transcription factor binding sites using an integrated model

Table 2 Detection of genes affected by RNAi using genome-wide Chromia predictions and ChIP-seq binding peaks

		Chen *et al*. [32]
	Number of genes affected by RNAi	Number of TF binding peaks		Chromia TP total number (promoters and enhancers) of predictions^†
TFs			TP*	3,600	8,000	12,000	20,000
Nanog	1,521	10,343	265 (17.4%)	199 (13.1%)	407 (26.8%)	568 (37.3%)	843 (55.4%)
Oct4	1,127	3,761	151 (13.4%)	170 (15.1%)	327 (29.0%)	452 (40.1%)	652 (57.8%)
Sox2	1,365	4,526	137 (10.0%)	195 (14.3%)	372 (27.3%)	529 (38.8%)	753 (55.1%)
Esrrb	871	21,647	376 (43.2%)	143 (16.4%)	256 (29.4%)	349 (40.1%)	476 (54.6%)

*A TF binding peak in the Chen et al. study [32] was considered to be a TP if it was within |W| = 10 kbp of an RNAi-affected gene's TSS. PPV is shown in parenthesis.^†The same number of predictions was made for promoters and enhancers. A promoter and an enhancer prediction were considered to be a TP if it was within |W| = 2 kbp for promoters and |W| = 10 kbp for enhancers of an RNAi-affected gene's TSS. The TP value from Chromia is shown in bold when it is larger than that from the Chen et al. study [32] but the number of Chromia predictions is smaller than the number of TF binding peaks determined in the Chen et al. study [32].

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