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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.

From: A combinatorial optimization approach for diverse motif finding applications

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