Table 3 Comparison of several computational methods for predicting TFBSs in the 20 genomic regions of sequences
From: Genome-wide prediction of transcription factor binding sites using an integrated model
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%) |