Table 1.
Overview of Crohn’s Disease analyses.
Table 2.
Number of significant genes at different p-value thresholds.
Fig 1.
Comparison of gene analysis results for different test-statistics.
Gene -log10 p-values from the CD data gene analysis in MAGMA for three different gene test-statistics, comparing analyses using (A) the mean χ2 statistic with the top χ2 statistic, (B) the mean χ2 statistic and the PC regression model and (C) the top χ2 statistic and the PC regression model. P-values below 10–8 are truncated to 10–8 (grey points) to preserve the visibility of the other points.
Fig 2.
Comparison of self-contained gene-set analysis results.
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.
Table 3.
Number of significant gene sets at different p-value thresholds.
Table 4.
Competitive gene-set p-values for MAGMA and INRICH significant gene-sets.
Fig 3.
Comparison of competitive gene-set analysis results.
Gene set -log10 p-values from the CD data competitive gene-set analysis for MAGMA, ALIGATOR, INRICH and MAGENTA. Results for ALIGATOR and INRICH are shown for each for the SNP p-value cutoff that yielded the highest observed power (0.01 and 0.0001 respectively), MAGENTA at the advised 5th percentile cutoff. P-values for gene sets not evaluated by one of the methods are shown in grey. The shown correlations are for the -log10 p-values for gene-sets evaluated by both methods.
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.
Table 5.
Computation times for gene and gene-set analyses.