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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