|
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.