Table 1 |
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|
Summary of functional tests of 466 predicted TF binding sites in four human cell lines |
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|
TF |
Func. |
Tested |
Ubq.Func. |
Ubq. Act. |
Ubq. Rep. |
Func. K562 |
Func. HCT116 |
Func HT1080 |
Func HepG2 |
PWM |
AUC |
|
|
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|
CTCF |
104 |
168 |
9 |
9 |
0 |
62 |
52 |
49 |
53 |
Ref. [31] |
0.84 |
|
E2F4 |
7 |
12 |
0 |
0 |
0 |
3 |
3 |
3 |
0 |
E2F:4 M00739 |
0.83 |
|
E2F6 |
2 |
3 |
0 |
0 |
0 |
1 |
0 |
1 |
0 |
E2F:1 M00938 |
0.78 |
|
EGR1 |
1 |
2 |
0 |
0 |
0 |
0 |
1 |
0 |
0 |
Egr:3 M00245 |
0.76 |
|
GABP |
7 |
11 |
4 |
4 |
0 |
5 |
5 |
6 |
5 |
Ref. [103] |
0.77 |
|
GATA1 |
4 |
4 |
1 |
1 |
0 |
4 |
4 |
1 |
1 |
GATA:1 M00128 |
0.69 |
|
GATA2 |
47 |
80 |
4 |
3 |
1 |
36 |
20 |
18 |
14 |
GATA:2 M00348 |
0.81 |
|
JUND |
3 |
3 |
1 |
1 |
0 |
2 |
2 |
1 |
3 |
CREBP1 M00041 |
0.65 |
|
MAX |
3 |
3 |
1 |
0 |
1 |
2 |
2 |
2 |
2 |
cMycMax M00118 |
0.77 |
|
STAT1 |
54 |
69 |
16 |
11 |
5 |
41 |
27 |
29 |
39 |
STAT1 M00224 |
0.74 |
|
USF1 |
2 |
2 |
1 |
1 |
0 |
2 |
2 |
2 |
1 |
USF M00121 |
0.86 |
|
YY1 |
86 |
98 |
26 |
9 |
16 |
63 |
56 |
53 |
58 |
Ref. [103] |
0.82 |
|
|
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|
Total |
320 |
455 |
63 |
39 |
23 |
221 |
174 |
165 |
176 |
||
|
|
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|
For each TF that was part of our functional study, columns list the number of functional verifications in at least one cell line, number of TFBSs tested, number of ubiquitously functional TFBSs, number of ubiquitously activating TFBSs, number of ubiquitously repressing TFBSs, number of TFBSs functionally verified in each cell line, the source of PWM used and the corresponding AUC when applied ChIP-seq data sets. The PWMs are shown as motif logos in Table S1 of Additional file 1. |
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|
Whitfield et al. Genome Biology 2012 13:R50 doi:10.1186/gb-2012-13-9-r50 |
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