Table 3 |
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|
Stepwise linear regression statistics |
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|
S. cerevisiae |
Three or more genomes |
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|
|
|
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|
Word |
Mfc |
p-value |
ΔR2 |
Mfc |
p-value |
ΔR2 |
p-value |
p-value |
|
|
|
|||||||||
|
Amino-acid starvation 0.5 h |
AAATTT |
-0.165 |
< 2.0e-16 |
3.1% |
-0.293 |
< 2.0e-16 |
6.6% |
1.3e-37 |
2.0e-07 |
|
GATGAG |
- |
- |
- |
-0.333 |
6.7e-16 |
4.1% |
1.6e-30 |
8.5e-03 |
|
|
AAGGGG |
0.209 |
3.2e-14 |
1.8% |
0.455 |
< 2.0e-16 |
3.5% |
1.6e-22 |
7.9e-05 |
|
|
TGTGGC |
0.094 |
1.1e-03 |
0.6% |
0.283 |
2.9e-07 |
1.6% |
5.0e-07 |
8.3e-13 |
|
|
CCCTTA |
0.300 |
2.0e-16 |
1.7% |
0.363 |
< 2.0e-16 |
1.4% |
3.2e-06 |
3.5e-03 |
|
|
TGACTC |
0.229 |
4.6e-10 |
0.8% |
0.311 |
2.2e-11 |
1.0% |
4.6e-01 |
1.1e-03 |
|
|
AAATTT • GATGAG |
- |
- |
- |
-0.266 |
9.1e-09 |
0.5% |
- |
- |
|
|
CACGTG |
0.045 |
3.5e-01 |
0.5% |
0.146 |
8.6e-03 |
0.5% |
1.9e-07 |
1.2e-08 |
|
|
CACGTG • TGTGGC |
0.443 |
3.8e-10 |
0.5% |
0.749 |
1.0e-12 |
0.9% |
- |
- |
|
|
GTGAAA |
-0.066 |
1.1e-03 |
0.3% |
-0.082 |
4.6e-03 |
0.1% |
- |
- |
|
|
TCTTTT |
-0.022 |
2.3e-02 |
0.1% |
- |
- |
- |
- |
- |
|
|
Total ΔR2 |
9.6% |
20.2% |
|||||||
|
Stationary phase YPD 10 h |
AAATTT |
-0.218 |
< 2.0e-16 |
3.2% |
-0.377 |
< 2.0e-16 |
5.8% |
5.5e-39 |
N/R |
|
AAGGGG |
0.233 |
1.7e-11 |
0.9% |
0.591 |
< 2.0e-16 |
4.0% |
4.5e-26 |
N/R |
|
|
CCCTTA |
0.460 |
< 2.0e-16 |
3.7% |
0.579 |
< 2.0e-16 |
2.2% |
3.0e-07 |
N/R |
|
|
GATGAG |
- |
- |
- |
-0.242 |
4.1e-06 |
1.8% |
4.4e-18 |
N/R |
|
|
ACCCCA |
0.224 |
3.0e-03 |
0.3% |
0.459 |
1.5e-06 |
1.0% |
- |
N/R |
|
|
AAATTT • GATGAG |
- |
- |
- |
-0.287 |
1.7e-06 |
0.4% |
- |
N/R |
|
|
CCGCCG |
0.333 |
5.1e-07 |
0.8% |
0.208 |
1.5e-02 |
0.3% |
- |
N/R |
|
|
ACCCCA • CCGCCG |
0.294 |
1.8e-02 |
0.1% |
0.807 |
5.6e-05 |
0.3% |
- |
N/R |
|
|
GTGAAA |
-0.090 |
4.2e-04 |
0.2% |
-0.122 |
1.0e-03 |
0.2% |
- |
N/R |
|
|
Total ΔR2 |
9.4% |
16.0% |
|||||||
|
Terbinafine 3 h |
TGACTC |
0.162 |
< 2.0e-16 |
3.5% |
0.261 |
< 2.0e-16 |
5.1% |
1.3e-14 |
N/R |
|
TCGTTT |
0.071 |
< 2.0e-16 |
2.0% |
0.132 |
< 2.0e-16 |
3.3% |
2.5e-24 |
N/R |
|
|
TGAAAC |
-0.055 |
1.3e-12 |
1.1% |
-0.077 |
9.50e-11 |
0.9% |
4.0e-03 |
N/R |
|
|
GATGAG |
-0.029 |
1.7e-03 |
0.3% |
-0.047 |
6.70e-06 |
0.4% |
- |
N/R |
|
|
AAGGGG |
0.025 |
1.1e-02 |
0.1% |
0.050 |
5.40e-04 |
0.3% |
2.4e-01 |
N/R |
|
|
CCGATA |
-0.008 |
6.5e-01 |
0.1% |
0.004 |
8.6e-01 |
0.1% |
- |
N/R |
|
|
CCGATA • TCGTTT |
0.080 |
9.4e-06 |
0.3% |
0.146 |
3.2e-07 |
0.5% |
- |
N/R |
|
|
CCCTTA |
-0.021 |
5.0e-02 |
0.1% |
-0.038 |
1.1e-02 |
0.1% |
- |
N/R |
|
|
Total ΔR2 |
7.6% |
10.8% |
|||||||
|
|
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|
Words and pairwise interaction terms are reported in the order of selection by the stepwise linear regression procedure performed on conserved words. The influence terms (Mf), associated p-values, and increase in R-square values were computed using the statistical package R [51]. Wang et al. [20] and Conlon et al. [21] previously fit regression models using sequence features derived from S. cerevisiae. The p-values of the most similar sequences features in their regression models were reported where available; sequence features that were more significant in this analysis are indicated in bold. Dashes indicate sequence features that were insignificant in the Wang et al. [20] or Conlon et al. [21] analyses. 'N/R' indicates gene-expression data that were not analyzed by Conlon et al. [21] |
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|
Chiang et al. Genome Biology 2003 4:R43 doi:10.1186/gb-2003-4-7-r43 |
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