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.

Korb et al. BMC Immunology 2008 9:7   doi:10.1186/1471-2172-9-7