Table 4.
Coverage values of modules on positive, negative and random datasets
| Regulatory module |
Positive promoter set |
Negative promoter set |
Random genomic set |
|||
|---|---|---|---|---|---|---|
| C+ | p-valuea | C– | Rankb | CR | Rankb | |
| 1 |
0.92 |
3.8E-23 |
0.0181 |
1 |
0.0155 |
1 |
| 2 |
0.92 |
8.8E-14 |
0.0776 |
8 |
0.0813 |
7 |
| 3 |
1 |
2.2E-20 |
0.0350 |
3 |
0.0308 |
4 |
| 4c |
1 |
6.5E-19 |
0.0362 |
5 |
0.0399 |
6 |
| 5 |
1 |
4.1E-19 |
0.0371 |
6 |
0.0385 |
5 |
| 6 |
1 |
3.4E-23 |
0.0360 |
4 |
0.0187 |
2 |
| 7 |
1 |
3.5E-14 |
0.1101 |
10 |
0.0922 |
9 |
| 8 |
1 |
1.9E-09 |
0.2018 |
11 |
0.2137 |
11 |
| 9 |
1 |
1.6E-13 |
0.1009 |
9 |
0.1035 |
10 |
| 10 |
0.77 |
5.9E-19 |
0.0200 |
2 |
0.0223 |
3 |
| 11 |
1 |
6.8E-15 |
0.0642 |
7 |
0.0813 |
8 |
| Add1 |
1 |
5.5E-31 |
0.0091 |
|
0.0047 |
|
| Add2 | 1 | 3.6E-47 | 0.0000 | 0.000267d | ||
ap-values are calculated as probability of 13*C+ successful hits out of 13 trials, with probability of success in one trial CR.
bRank is according to the ratio C+/C– and C+/CR respectively.
cFunctional module 4 does not rank high according to its p-value. One can easily find motifs combinations exhibiting superior statistics (for example, Add1 (Meme1 + Meme4 + TGIF) or Add2 (Meme1 + Meme2 + Meme5).
dTo calculate this value, another random sequence set was generated by repeating 10 times the procedure of random splitting the Salmonella genome. In total the module can be found on 21 of such sequences.