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Table 1 Assessment of the genome-wide TFBS predictions when |W| = 1,000 bp

From: Genome-wide prediction of transcription factor binding sites using an integrated model

 

Chromia TP (PPV)

TF

Promoters

Enhancers

CTCF

319 (16.0%)

195 (9.8%)

E2f1

1,920 (96.0%)

618 (30.9%)

Esrrb

585 (29.2%)

491 (24.6%)

Klf4

917 (45.9%)

351 (17.5%)

Nanog

138 (6.9%)

376 (18.8%)

Myc (n-Myc + c-Myc)

1,436 (71.8%)

167 (8.3%)

Oct4

240 (12.0%)

208 (10.4%)

Oct4-Sox2-Nanog

384 (19.2%)

431 (21.6%)

Smad1

6 (0.3%)

95 (4.8%)

Sox2

63 (3.1%)

235 (11.8%)

STAT3

99 (5.0%)

82 (4.1%)

Tcfcp2l1

716 (35.8%)

595 (29.8%)

Zfx

1,320 (66.0%)

219 (10.9%)

  1. A prediction was considered to be a true positive (TP) if it was within |W| = 1,000 bp of a TF binding peak. The total number of predictions is 2,000.
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Genome Biology

ISSN: 1474-760X

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