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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.
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BMC Bioinformatics

ISSN: 1471-2105

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