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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]