Table 4 |
|||||||||
|
Results |
|||||||||
|
Data set |
True Positives |
False Positives |
True Negatives |
False Negatives |
Precision |
Recall |
F1 Score |
p-value |
|
|
|
|||||||||
|
Lee et al. |
GAT3, RGM1 |
5 |
22 |
78 |
10 |
0.185 |
0.333 |
0.238 |
0.253 |
|
GAL4, YAP5 |
7 |
16 |
84 |
9 |
0.304 |
0.438 |
0.359 |
0.0169 |
|
|
GAT3, PDR1 |
10 |
9 |
91 |
7 |
0.526 |
0.588 |
0.556 |
1.138e-05 |
|
|
CIN5, NRG1 |
10 |
18 |
82 |
8 |
0.357 |
0.556 |
0.435 |
1.53e-03 |
|
|
RGM1, YAP5 |
7 |
13 |
87 |
11 |
0.35 |
0.389 |
0.368 |
0.0137 |
|
|
NDD1, SWI4 |
15 |
23 |
77 |
7 |
0.395 |
0.682 |
0.5 |
8.51e-05 |
|
|
SKN7, SWI4 |
12 |
38 |
62 |
10 |
0.24 |
0.545 |
0.333 |
0.118 |
|
|
PDR1, YAP5 |
13 |
36 |
64 |
10 |
0.265 |
0.565 |
0.361 |
0.0585 |
|
|
FKH2, SWI4 |
11 |
20 |
80 |
13 |
0.355 |
0.458 |
0.4 |
0.0113 |
|
|
PHD1, YAP6 |
14 |
18 |
82 |
10 |
0.438 |
0.583 |
0.5 |
1.52-e04 |
|
|
FHL1, YAP5 |
15 |
19 |
81 |
10 |
0.441 |
0.6 |
0.508 |
1.07-e04 |
|
|
FKH2, MCM1 |
20 |
33 |
67 |
5 |
0.377 |
0.8 |
0.513 |
2.45-e05 |
|
|
MBP1, NDD1 |
13 |
24 |
76 |
12 |
0.351 |
0.52 |
0.419 |
7.52-e03 |
|
|
ACE2, SWI5 |
17 |
29 |
71 |
9 |
0.37 |
0.654 |
0.472 |
7.97-e04 |
|
|
FKH2, MBP1 |
19 |
31 |
69 |
8 |
0.38 |
0.704 |
0.494 |
2.60-e04 |
|
|
MCM1, NDD1 |
24 |
36 |
64 |
4 |
0.4 |
0.857 |
0.545 |
2.37-e06 |
|
|
RAP1, YAP5 |
15 |
7 |
93 |
14 |
0.682 |
0.517 |
0.588 |
3.68-e07 |
|
|
NRG1, YAP6 |
15 |
22 |
78 |
15 |
0.405 |
0.5 |
0.448 |
3.72-e03 |
|
|
GAT3, YAP5 |
25 |
11 |
89 |
14 |
0.694 |
0.641 |
0.667 |
8.75-e10 |
|
|
CIN5, YAP6 |
26 |
41 |
59 |
14 |
0.388 |
0.65 |
0.486 |
8.47-e03 |
|
|
MBP1, SWI4 |
27 |
33 |
67 |
13 |
0.45 |
0.675 |
0.54 |
2.00-e04 |
|
|
SWI4, SWI6 |
20 |
45 |
55 |
23 |
0.308 |
0.465 |
0.37 |
0.506 |
|
|
MBP1, SWI6 |
39 |
38 |
62 |
5 |
0.506 |
0.886 |
0.645 |
6.34-e09 |
|
|
FKH2, NDD1 |
35 |
83 |
17 |
15 |
0.297 |
0.7 |
0.417 |
0.978 |
|
|
FHL1, RAP1 |
89 |
36 |
64 |
25 |
0.712 |
0.781 |
0.745 |
3.33-e10 |
|
|
|
|||||||||
|
Gasch et al. |
iESR |
89 |
453 |
4497 |
181 |
0.164 |
0.33 |
0.219 |
~0 |
|
rESR_PACcluster |
173 |
260 |
4690 |
255 |
0.4 |
0.404 |
0.402 |
~0 |
|
|
rESR_RPcluster |
50 |
84 |
4866 |
71 |
0.373 |
0.413 |
0.392 |
~0 |
|
|
|
|||||||||
|
Sinha et al. |
Yeast |
6 |
2 |
7 |
0 |
0.75 |
1 |
0.857 |
5.59-e03 |
|
|
|||||||||
|
Sinha et al. |
Fly |
3 |
3 |
97 |
5 |
0.5 |
0.375 |
0.429 |
4.92-e03 |
|
Sinha et al. |
Fly, known PWMs |
7 |
10 |
90 |
1 |
0.412 |
0.875 |
0.560 |
5.10e-06 |
|
|
|||||||||
|
Results of running our algorithm on the data in Table 3. Significant CRMs (p-value < 0.01) are indicated with bold text. |
|||||||||
|
Noto and Craven BMC Bioinformatics 2006 7:528 doi:10.1186/1471-2105-7-528 |
|||||||||
