Table 2.

Comparison of IIDB TFBS predictions with ChIP-chip data. Data are presented based on the genome annotations available from both NCBI and ENSEMBL. Note that the annotations differ in the number of predicted genes.

	Using NCBI coordinates				Using ENSEMBL coordinates
Promoter region mapped †	1000	2000	1000	2000	1000	2000	1000	2000
Number of genes	1151	1151	1151	1151	1935	1935	1935	1935
Unique ATF3 ChIP-chip hits	978	1761	978	1761	1494	2750	1494	2750
Conserved promoter regions containing ATF3 TFBS ◇	833	979	833	979	1329	1550	1329	1550
Percentile threshold ■	0.05	0.05	0.01	0.01	0.05	0.05	0.01	0.01
ATF3-group matrices hits*	792	1187	212	299	1333	2029	337	474
ATF3-group matrices within a ChIP-chip segment	442	664	110	165	710	1031	196	272
%overlap between ChIP-chip data & predictions ◉	55.8	55.9	51.8	55.2	53.2	50.8	58.1	57.4

Notes: ◇ Conserved regions were mapped from the human data of Xie et.al [14]. ■ Threshold refers to the p-value below which predicted TFBS are considered significant. † Numbers refer to length of promoter annotated, in base pairs upstream of the transcription start site. * Since ATF3 binding sites have a strong overlap with CREB binding sites, we used a combined PWM including three ATF matrices and nine CREB matrices to calculate the ATF3 hits. Overlapping hits were collapsed into one as described in the main text. ◉ ChIP fragments in these experiments were estimated to have an average length of approximately 500 bp to 1 Kbp. To determine the coordinates of a ChIP-chip hit, we estimated the center of gravity of a bound region using a moving average filter, then set the start/end coordinates to be +/- 300 bp.