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Table 1 Pathway analysis methods investigated in this study

From: Identifying significantly impacted pathways: a comprehensive review and assessment

  Method Category R-function/package version Pathway database
1 Fisher’s exact test non-TB fisher.test KEGG v.65
2 WebGestalt non-TB WebGestaltR 0.3.1 KEGG v.65
3 GOstats non-TB 2.48.0 KEGG v.65
4 Kolmogorov-Smirnov test non-TB ks.test KEGG v.65
5 Wilcoxon rank sum non-TB wilcox.test KEGG v.65
6 GSEA non-TB 1.0 KEGG v.65
7 GSA non-TB 1.03 KEGG v.65
8 PADOG non-TB 1.20.0 KEGG v.65
9 SPIA TB 2.30.0 KEGG v.65
10 ROntoTools TB 2.6.0 KEGG v.65
11 CePaORA TB 0.5 KEGG (version unknown)
12 CePaGSA TB 0.5 KEGG (version unknown)
13 PathNet TB 1.18.0 KEGG v.56
  1. Versions of KEGG of CePa methods are unknown because they are embedded in the software
  2. non-TB non-topology-based method, TB topology-based method