| | |
S. cerevisiae
|
Three or more genomes
| | |
|---|
| |
Word
|
M
fc
|
p-value
|
ΔR2
|
M
fc
|
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%
| | |
- 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 (M
f
), 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]
