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Table 1 Yeast cell cycle results. PCGSE computed enrichment p-values for the Spellman et al. [39] yeast cell cycle gene sets relative to the first two PCs of the Spellman et al. α factor-synchronized gene expression data processed using the steps outlined in Alter et al. [5]. PCGSE was executed using Fisher transformed Pearson correlation coefficients between genes and PCs as gene-level test statistics

From: Principal component gene set enrichment (PCGSE)

 

T-test

Cor-adj t-test

Perm

 

PC 1

PC 2

PC 1

PC 2

PC 1

PC 2

M/G1

0.68

1.2e-12

0.94

0.18

0.94

0.22

G 1

3.5e-130

1e-35

0.023

0.23

0.024

0.35

S

1e-10

0.0074

0.2

0.59

0.2

0.62

S/G2

0.27

4.6e-06

0.86

0.45

0.87

0.47

G2/M

8.3e-38

0.068

0.07

0.79

0.048

0.81

  1. Significance of the \({S^{D}_{k}}\) gene set statistic was computed using either a two-sided t-test, a correlation-adjusted two-sided t-test or a two-sided permutation test
  2. Unadjusted p-values less than 0.05 are displayed in bold