Skip to main content

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