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Table 4 Performance of TFBS prediction methods using the PWMs derived using rGADEM and ENCODE-ChIP-Seq data

From: Evaluating tools for transcription factor binding site prediction

  Sn PPV ACC g FPR s
CLUSTER     
Baycis 0.792 0.687 0.738 0.021
Cister 0.828 0.722 0.773 0.022
MCast 0.907 0.778 0.840 0.013
Comet 0.871 0.759 0.813 0.014
ClusterBuster 0.849 0.739 0.792 0.017
INDIVIDUAL     
Matrix-Scan 0.830 0.717 0.771 0.018
Clover 0.851 0.736 0.791 0.015
FIMO 0.933 0.839 0.884 0.002
Patser 0.887 0.774 0.828 0.008
PossumSearch 0.875 0.758 0.814 0.010
  1. Average sensitivities (Sn), Positive Predictive Value (PPV) and accuracy (ACC g ) are reported together with the false positive rate using scrambled sequences (FPR s ). Performance was evaluated across the 12 PWMs that could be derived from the ENCODE-ChIP-Seq data using rGADEM that have validated TFBSs in PAZAR (the PAZAR-E dataset). The best performing tools, MCast and FIMO are highlighted in bold