Comparison of self-contained gene-set analysis results.

<p>Gene set—log10 p-values from the CD data self-contained gene-set analysis for MAGMA and PLINK. Panel (A) shows the PLINK-avg (no pruning) results compared with the MAGMA-main analysis, panel (B) the PLINK-prune results compared with the MAGMA-main analysis and (C) the two PLINK analyses compared to each other. P-values below 10^–8 are truncated to 10^–8 (grey points) to preserve the visibility of the other points.