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Variants that showed different effects on CVD-related quantitative traits in women and men are shown in Table 6, using an interaction p-value cut off ≤0.01 and an association cut off p<0.01 in either women or men in combined analysis of both cohorts.
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We identified 3 variants displaying effect differences between the cohorts using genotype-cohort interaction analysis (interaction p-value <0.05), and they were removed.
Interaction p-value: 0.0032.
***NSAID*APOE-ε4 interaction p-value = 0.04.
In addition, a parametric bootstrap test was used to estimate interaction P-values adjusted for multiple testing [ 15].
A global interaction P value was used to identify associations with metabolic markers that differed significantly in effect size between men and women.
There were no statistically significant time-by-variable interactions observed using a p-value cutoff of 0.10.
Effect modification was considered for age and educational level measured at baseline, using a p-value <0.1 of the interaction term to indicate effect modification.
The results depicted in Figure 6a and 6b suggest that GAP outperforms existing systems in extracting the experimentally known protein direct/indirect interactions (p-value < 2.96E-08 using Wilcoxon rank sum tests on AUC scores when comparing GAP with each of the individual tools).
Two-way interactions between the selected candidate factors are tested in a second step in which the false discovery rate (FDR, the expected proportion of false positives to the total number of positives) is estimated using a parametric bootstrap method which involves estimating interaction p-values under the null hypothesis of no interaction.
We used the FDR method to adjust interaction p-values for multiple comparisons.
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