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Table 2 Comparison between gene set analysis methods in terms of sensitivity and pathway ranking when analyzing 143 KEGG non-metabolic pathways

From: Down-weighting overlapping genes improves gene set analysis

  GSEA GSA PADOG
p geometric mean 0.2846 0.1516 0.0585
p median 0.2468 0.147 0.1225
% p<0.05 0 12.5 33.3
% q<0.05 0 0 4.2
rank mean 42.31 28.64 21.45
rank median 35.84 21.15 14.69
Wilcoxon p 0.9885 reference 0.0007
LME p 0.9909 reference 0.0008
LME coefficient 13.67 reference -7.20
  1. The table shows statistics computed from nominal and adjusted p-values, and ranks of the 24 target pathways only, including geometric mean, median and percentages of pathways significant at 0.05 level based on nominal and adjusted p-values (q-values). The results of comparing the ranks of each method against GSA method (chosen as reference), using a paired Wilcoxon test and a linear mixed-effects model, are included. The best value for each criterion is shown in bold.