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Table 3 Stepwise linear regression statistics

From: Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts

  

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%

  
  1. 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]
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Genome Biology

ISSN: 1474-760X

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