 
S. cerevisiae

Three or more genomes
  


Word

M
_{
fc
}

pvalue

ΔR^{2}

M
_{
fc
}

pvalue

ΔR^{2}

pvalue

pvalue


Aminoacid starvation 0.5 h

AAATTT

0.165

< 2.0e16

3.1%

0.293

< 2.0e16

6.6%

1.3e37

2.0e07


GATGAG







0.333

6.7e16

4.1%

1.6e30

8.5e03


AAGGGG

0.209

3.2e14

1.8%

0.455

< 2.0e16

3.5%

1.6e22

7.9e05


TGTGGC

0.094

1.1e03

0.6%

0.283

2.9e07

1.6%

5.0e07

8.3e13


CCCTTA

0.300

2.0e16

1.7%

0.363

< 2.0e16

1.4%

3.2e06

3.5e03


TGACTC

0.229

4.6e10

0.8%

0.311

2.2e11

1.0%

4.6e01

1.1e03


AAATTT • GATGAG







0.266

9.1e09

0.5%






CACGTG

0.045

3.5e01

0.5%

0.146

8.6e03

0.5%

1.9e07

1.2e08


CACGTG • TGTGGC

0.443

3.8e10

0.5%

0.749

1.0e12

0.9%






GTGAAA

0.066

1.1e03

0.3%

0.082

4.6e03

0.1%






TCTTTT

0.022

2.3e02

0.1%












Total ΔR^{2}
  
9.6%
  
20.2%
  
Stationary phase YPD 10 h

AAATTT

0.218

< 2.0e16

3.2%

0.377

< 2.0e16

5.8%

5.5e39

N/R


AAGGGG

0.233

1.7e11

0.9%

0.591

< 2.0e16

4.0%

4.5e26

N/R


CCCTTA

0.460

< 2.0e16

3.7%

0.579

< 2.0e16

2.2%

3.0e07

N/R


GATGAG







0.242

4.1e06

1.8%

4.4e18

N/R


ACCCCA

0.224

3.0e03

0.3%

0.459

1.5e06

1.0%



N/R


AAATTT • GATGAG







0.287

1.7e06

0.4%



N/R


CCGCCG

0.333

5.1e07

0.8%

0.208

1.5e02

0.3%



N/R


ACCCCA • CCGCCG

0.294

1.8e02

0.1%

0.807

5.6e05

0.3%



N/R


GTGAAA

0.090

4.2e04

0.2%

0.122

1.0e03

0.2%



N/R


Total ΔR^{2}
  
9.4%
  
16.0%
  
Terbinafine 3 h

TGACTC

0.162

< 2.0e16

3.5%

0.261

< 2.0e16

5.1%

1.3e14

N/R


TCGTTT

0.071

< 2.0e16

2.0%

0.132

< 2.0e16

3.3%

2.5e24

N/R


TGAAAC

0.055

1.3e12

1.1%

0.077

9.50e11

0.9%

4.0e03

N/R


GATGAG

0.029

1.7e03

0.3%

0.047

6.70e06

0.4%



N/R


AAGGGG

0.025

1.1e02

0.1%

0.050

5.40e04

0.3%

2.4e01

N/R


CCGATA

0.008

6.5e01

0.1%

0.004

8.6e01

0.1%



N/R


CCGATA • TCGTTT

0.080

9.4e06

0.3%

0.146

3.2e07

0.5%



N/R


CCCTTA

0.021

5.0e02

0.1%

0.038

1.1e02

0.1%



N/R


Total ΔR^{2}
  
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 pvalues, and increase in Rsquare 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 pvalues 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 geneexpression data that were not analyzed by Conlon et al. [21]