Table 3 Correlation for pathway-level results between rankings within each method and the proportion of associated genes within the pathway using only the 10 larger pathways evaluated, as well as correlation with mean ranking across all programs
Group | Method | Citation | Input | Correlation with causal proportion | Correlation with mean ranking |
|---|---|---|---|---|---|
(95% CI) | (95% CI) | ||||
Competitive | ALIGATOR | [24] | SNP P-values | −0.6 (−0.89, 0.05) | 0.75 (0.22, 0.94) |
GenGen | [25] | SNP P-values | −0.64 (−0.91, −0.02) | 0.82 (0.41, 0.96) | |
GSA-SNP | [21] | SNP P-values | −0.59 (−0.89, 0.06) | 0.78 (0.28, 0.94) | |
GSEA-SNP | [22] | Raw Genotypes | −0.6 (−0.89, 0.04) | 0.73 (0.18, 0.93) | |
MAGENTA | [20] | SNP P-values | −0.63 (−0.9, 0) | 0.9 (0.62, 0.98) | |
MGFM | [26] | SNP P-values | −0.53 (−0.87, 0.15) | 0.7 (0.13, 0.92) | |
SRT | [27] | Raw Genotypes | −0.43 (−0.84, 0.27) | 0.55 (−0.12, 0.88) | |
Self-Contained | GRASS | [23] | Raw Genotypes | −0.49 (−0.86, 0.2) | 0.53 (−0.15, 0.87) |
HYST | [18] | SNP P-values | −0.57 (−0.88, 0.09) | 0.84 (0.46, 0.96) | |
PST | [11] | Raw Genotypes | −0.26 (−0.76, 0.44) | 0.55 (−0.12, 0.88) |