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Table 2 Detection of genes affected by RNAi using genome-wide Chromia predictions and ChIP-seq binding peaks

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

   Chen et al. [32]     
  Number of genes affected by RNAi Number of TF binding peaks   Chromia TP total number (promoters and enhancers) of predictions
TFs    TP* 3,600 8,000 12,000 20,000
Nanog 1,521 10,343 265 (17.4%) 199 (13.1%) 407 (26.8%) 568 (37.3%) 843 (55.4%)
Oct4 1,127 3,761 151 (13.4%) 170 (15.1%) 327 (29.0%) 452 (40.1%) 652 (57.8%)
Sox2 1,365 4,526 137 (10.0%) 195 (14.3%) 372 (27.3%) 529 (38.8%) 753 (55.1%)
Esrrb 871 21,647 376 (43.2%) 143 (16.4%) 256 (29.4%) 349 (40.1%) 476 (54.6%)
  1. *A TF binding peak in the Chen et al. study [32] was considered to be a TP if it was within |W| = 10 kbp of an RNAi-affected gene's TSS. PPV is shown in parenthesis.The same number of predictions was made for promoters and enhancers. A promoter and an enhancer prediction were considered to be a TP if it was within |W| = 2 kbp for promoters and |W| = 10 kbp for enhancers of an RNAi-affected gene's TSS. The TP value from Chromia is shown in bold when it is larger than that from the Chen et al. study [32] but the number of Chromia predictions is smaller than the number of TF binding peaks determined in the Chen et al. study [32].