Skip to main content

Table 3 Comparison between pathway analysis methods in terms of sensitivity and pathway ranking when analyzing 229 KEGG metabolic and non-metabolic pathways

From: Down-weighting overlapping genes improves gene set analysis

p geometric mean 0.2846 0.1387 0.0485
p median 0.2468 0.142 0.091
% p<0.05 0 16.7 33.3
% q<0.05 0 0 4.2
rank mean 41.42 26.97 18.95
rank med 38.43 16.7 13.05
Wilcoxon p 0.9956 reference 0.0006
LME p 0.9962 reference 0.0023
LME coefficient 14.45 reference -8.02
  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.