Table 2  Listing of the transcription factors' datasets (columns 1, 2, and 3) and the results of motif finding by LP/DEE. TF is the transcription factor dataset. Seq is the number of input sequences. Len is the length of the motif searched for. The rest of the listed measures refer to the motifs discovered by the LP/DEE algorithm: IC is the average per-column information content [44]; RE is the average per-column relative entropy; E-value is the e-value, computed according to our statistical significance assessment; nPC is the nucleotide level performance coefficient; and sSn is the site level sensitivity. The four starred entries indicate potentially non-optimal solutions; entries marked with † indicated usage of the ILP solver.
TF   Seq   Len   IC   RE   E-value   nPC   sSn
ada  3  31  1.3000  1.0846  9.16 × 10-1  0.1341  0.33
araC  4  48  1.1437  0.9940  1.15 × 10-3  0.3474  0.50
arcA  11  15  1.2505  1.1992  4.31 × 10-6  0.4224  0.73
argR  8  18  1.2990  1.2149  1.30 × 10-7  0.2857  0.50
cpxR  7  15  1.3290  1.2337  1.09 × 10-5  0.5556  0.71
crp*†  33  18  0.7196  0.7045  3.08 × 10-9  0.5570  0.76
cytR  5  18  1.2317  1.1069  2.48 × 10-1  0.0588  0.20
dnaA  6  15  1.4535  1.3300  6.12 × 10-6  1.0000  1.00
fadR  5  17  1.3466  1.2074  1.33 × 10-2  0.5455  0.80
fis*  8  35  0.8927  0.8376  1.37 × 10-6  0.1966  0.38
flhCD  3  31  1.3942  1.1656  4.79 × 10-3  0.0000  0.00
fnr  10  22  1.1025  1.0476  1.85 × 10-9  0.6176  0.80
fruR  10  16  1.2094  1.1491  5.52 × 10-8  0.8182  0.90
fur  7  18  1.3285  1.2332  1.28 × 10-8  0.4237  0.71
galR  7  16  1.5445  1.4347  1.52 × 10-16  0.5034  0.71
glpR  4  20  1.4227  1.2441  2.63 × 10-2  0.5534  0.75
hns  5  11  1.5175  1.3660  2.25  0.0000  0.00
ihf*  19  48  0.3932  0.3859  2.26 × 10+8  0.0381  0.16
lexA  17  20  1.1481  1.1192  1.01 × 10-40  0.7215  0.88
lrp  4  25  1.2879  1.1237  6.44 × 10-2  0.0989  0.25
malT  6  10  1.5071  1.3815  1.73 × 10-1  0.0000  0.00
metJ  5  16  1.6842  1.5195  3.37 × 10-12  0.6495  1.00
metR  6  15  1.3097  1.1970  6.57 × 10-2  0.0000  0.00
modE  3  24  1.5618  1.3145  3.95 × 10-4  1.0000  1.00
nagC  5  23  1.2795  1.1462  1.03 × 10-3  0.0360  0.20
narL  10  16  1.1391  1.0828  8.06 × 10-4  0.8182  0.90
narP  4  16  1.4534  1.2737  7.48 × 10-4  0.0000  0.00
ntrC  4  17  1.6621  1.4605  1.28 × 10-8  0.6386  1.00
ompR  4  20  1.3566  1.1860  4.27 × 10-6  0.0000  0.00
oxyR  4  39  1.0965  0.9521  2.64  0.0796  0.25
phoB  8  22  1.1567  1.0835  4.14 × 10-9  0.8051  1.00
purR  20  26  0.8305  0.8147  1.53 × 10-37  0.7247  0.95
soxS*†  11  35  0.7771  0.7453  1.26 × 10-9  0.0815  0.27
trpR  4  24  1.4069  1.2291  3.74 × 10-6  0.8462  1.00
tus  5  23  1.5839  1.4276  1.05 × 10-17  0.8400  1.00
tyrR  10  22  1.0693  1.0159  3.63 × 10-9  0.5017  0.70