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