MAGMA: Generalized Gene-Set Analysis of GWAS Data
Fig 4
Comparison of competitive gene-set analysis results at different SNP cut-offs.
Comparison of gene set -log10 p-values from the CD data competitive gene-set analysis at different SNP p-value cut-offs for ALIGATOR (top row), INRICH (middle row) and MAGENTA (bottom row). The highest cut-off on the horizontal axis is compared to each of the lower cut-offs. P-values for gene sets not evaluated at the lower cut-off are shown in grey. The shown correlations are for the -log10 p-values for gene-sets evaluated at both cut-offs. Horizontal and vertical grey dotted lines demarcate the p = 0.05 nominal significance threshold.