Figure 4
From: GWIS - model-free, fast and exhaustive search for epistatic interactions in case-control GWAS
Example of a pair of individually insignificant SNPs in HT data. Example of a pair of individually insignificant SNPs in HT data that combined display both strong protective and contributing effects. Panel (a) shows prevalence mapping ROC curves for the pair (red) and individual SNPs (blue, green). Panels (b) and (c) zoom into the protective (top-right 20%) and contributory (lower-left 20%) areas respectively. Panel (d) shows selected statistics for the pair. The nine rows correspond to possible genotype calls for the pair of SNPs. Columns are: fltSS - the sensitivity-specificity filter score; fltGSS - the gain filter score; OR - Odds-Ratio; p 0 - percentage of Controls for the genotype call in this row; p 1 - percentage of Cases; spe% - specificity %; sen% - sensitivity %; RelRisk - relative risk for the genotype call := p 1/p 0; g1, g2 - genotype calls for the pair of SNPs; prevPerm - prevalence permutation (see Additional File Section 1.2). The genotype call (1, 0) (row 1) segregates 5.79% of Cases with only 0.24% of Controls resulting in an odds ratio of 25.73, fltSS = 37.81 and fltGSS = 33.83. Conversely, genotype calls {(1, 1), (2, 1)} (rows 8 and 9) cover 7.39% of Controls with only 0.41% of Cases resulting in an odds ratio of 0.05. This combination is also highly significant with fltSS = 39.74 and fltGSS = 35.9. The two points corresponding to these calls are highlighted with stars.