Table 3

Comparison of several computational methods for predicting TFBSs in the 20 genomic regions of sequences

TF

Chromia

Cluster-Buster

EEL

MCAST

Stubb single

Stubb multiple

CTCF

79/521 (13.2%)

215/352 (37.9%)

20/19 (51.3%)

251/320 (44.0%)

24/155 (13.4%)

21/524 (3.9%)

E2f1

512/88 (85.3%)

7/550 (1.3%)

0/19 (0.0%)

3/578 (0.5%)

69/508 (12.0%)

48/509 (8.2%)

Esrrb

141/459 (23.5%)

28/542 (4.9%)

3/28 (9.7%)

94/486 (16.2%)

52/323 (13.9%)

27/504 (5.1%)

Klf4

205/395 (34.2%)

2/574 (0.3%)

2/33 (5.7%)

74/518 (12.5%)

165/412 (28.6%)

50/479 (9.5%)

Myc

347/253 (57.8%)

2/563 (0.4%)

3/39 (7.1%)

19/559 (3.3%)

76/301 (20.2%)

94/433 (17.8%)

Nanog

47/553 (7.8%)

2/554 (0.4%)

0/21 (0.0%)

4/571 (0.7%)

4/283 (1.4%)

1/550 (0.18%)

Oct4

90/510 (15.0%)

16/546 (2.8%)

0/44 (0.0%)

19/526 (3.5%)

1/192 (0.5%)

0/528 (0.0%)

Oct4-Sox2-Nanog

120/480 (120%)

22/541 (3.9%)

0/45 (0.0%)

8/551 (1.4%)

3/152 (1.9%)

6/501 (1.2%)

Smad1

6/594 (1.0%)

2/564 (0.4%)

0/33 (0.0%)

1/571 (0.2%)

0/188 (0.0%)

0/506 (0.0%)

Sox2

25/575 (4.2%)

14/560 (2.4%)

0/37 (0.0%)

16/551 (2.8%)

1/500 (0.2%)

1/120 (0.8%)

STAT3

6/594 (1.0%)

1/555 (0.2%)

0/34 (0.0%)

9/567 (1.6%)

3/99 (2.9%)

4/522 (0.8%)

Tcfcp2l1

203/397 (33.8%)

66/506 (11.5%)

2/38 (5.0%)

156/417 (27.2%)

10/69 (12.7%)

28/496 (5.3%)

Zfx

310/290 (51.7%)

1/560 (0.2%)

2/34 (5.6%)

146/443 (24.8%)

268/303 (46.9%)

140/398 (26.0%)

TP, FP and PPV (PPV = TP/(TP + FP)) are listed for each TF using every method.

Won et al. Genome Biology 2010 11:R7   doi:10.1186/gb-2010-11-1-r7