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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.

From: The Innate Immune Database (IIDB)

  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
  1. 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.