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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

 

GSEA

GSA

PADOG

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.