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Table 6 Experiments on the 8 real datasets (2).

From: Discovering multiple realistic TFBS motifs based on a generalized model

Datasets MEME Weeder FlexModule
  sPPV sSn sF sPPV sSn sF sPPV sSn sF
CREB      medium     
R 1 0.73 0.58 0.65 0.44 0.84 0.58 0.68 ± 0.04 0.76 ± 0.04 0.72 ± 0.04
R 2 0.83 0.53 0.65 0.44 0.84 0.58 0.62 ± 0.22 0.69 ± 0.24 0.65 ± 0.23
R 3 0.83 0.53 0.65 0.44 0.84 0.58 0.67 ± 0.07 0.72 ± 0.07 0.69 ± 0.07
CRP      large     
R 1 0.93 0.61 0.74 0.41 0.71 0.52 0.94 ± 0.14 0.55 ± 0.11 0.69 ± 0.12
R 2 0.89 0.70 0.78 0.41 0.71 0.52 0.97 ± 0.07 0.56 ± 0.06 0.70 ± 0.06
R 3 0.89 0.70 0.78 0.41 0.71 0.52 0.96 ± 0.13 0.50 ± 0.10 0.65 ± 0.11
ERE      large     
R 1 0.88 0.60 0.71 0.29 0.64 0.40 0.74 ± 0.03 0.85 ± 0.01 0.79 ± 0.02
R 2 0.88 0.60 0.71 0.29 0.64 0.40 0.73 ± 0.02 0.85 ± 0.02 0.79 ± 0.02
R 3 0.88 0.60 0.71 0.29 0.64 0.40 0.68 ± 0.17 0.77 ± 0.24 0.72 ± 0.21
E2F      large     
R 1 0.78 0.67 0.72 0.23 0.93 0.37 0.56 ± 0.28 0.58 ± 0.29 0.57 ± 0.28
R 2 0.83 0.70 0.76 0.23 0.93 0.37 0.60 ± 0.29 0.60 ± 0.29 0.60 ± 0.29
R 3 0.78 0.67 0.72 0.23 0.93 0.37 0.63 ± 0.25 0.62 ± 0.25 0.63 ± 0.25
MEF2      medium     
R 1 0.93 0.82 0.88 0.01 0.06 0.02 0.86 ± 0.02 1.00 ± 0.00 0.93 ± 0.01
R 2 0.93 0.82 0.88 0.01 0.06 0.02 0.79 ± 0.27 0.90 ± 0.31 0.84 ± 0.29
R 3 0.93 0.82 0.88 0.01 0.06 0.02 0.88 ± 0.02 0.99 ± 0.04 0.93 ± 0.02
MyoD      small     
R 1 0.00 0.00 0.00 0.07 0.10 0.08 0.00 ± 0.00 0.00 ± 0.00 0.00 ± 0.00
R 2 0.00 0.00 0.00 0.07 0.10 0.08 0.00 ± 0.00 0.00 ± 0.00 0.00 ± 0.00
R 3 0.00 0.00 0.00 0.07 0.10 0.08 0.00 ± 0.00 0.00 ± 0.00 0.00 ± 0.00
SRF      large     
R 1 0.65 0.86 0.74 0.54 0.63 0.58 0.64 ± 0.00 0.87 ± 0.02 0.73 ± 0.01
R 2 0.70 0.86 0.78 0.54 0.63 0.58 0.63 ± 0.01 0.82 ± 0.05 0.71 ± 0.02
R 3 0.70 0.86 0.78 0.54 0.63 0.58 0.64 ± 0.00 0.86 ± 0.01 0.74 ± 0.00
TBP      small     
R 1 0.70 0.67 0.69 0.56 0.90 0.69 0.47 ± 0.32 0.59 ± 0.40 0.53 ± 0.35
R 2 0.70 0.67 0.69 0.56 0.90 0.69 0.41 ± 0.34 0.51 ± 0.42 0.45 ± 0.38
R 3 0.70 0.67 0.69 0.56 0.90 0.69 0.45 ± 0.34 0.55 ± 0.41 0.49 ± 0.37
Average 0.71 0.61 0.65 0.32 0.60 0.40 0.61 0.63 0.61
  1. Average results of MEME, Weeder and FlexModule in the same comparison experiments described in Table 5. Weeder was run with the width mode (small: 6, 8; medium: 6, 8, 10; large 6, 8, 10, 12) that are closest to the ranges R for each dataset.