Table 1 Pathway analysis methods investigated in this study
From: Identifying significantly impacted pathways: a comprehensive review and assessment
| Â | 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 |