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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.
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BMC Immunology

ISSN: 1471-2172

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