Table 6.

Results of the prostate cancer data example described in Section 6 for testing for the individual gene effects in the presence of possible gene-gene interactions (epistasis) in the cell growth pathway. Displayed are the p-values of the proposed garrote kernel machine test using the Gaussian kernel: (p_Gauss denotes the original GKM test and p_Gauss,PCA denotes the PCA based modified test) and the two-way interaction kernel (p_Two-way). Also reported in columns 5–7 are the adjusted p-values for multiple comparison using our permutation method proposed in Section 4.

Name	pGauss	pGauss,PCA	pTwo-way	$p_{\text{Gauss}}^{\ast }$	$p_{\text{Gauss},\text{PCA}}^{\ast }$	$p_{\text{Two}-\text{way}}^{\ast }$
MYBL2	0.287	0.335	0.066	0.832	0.861	0.235
FGF2	0.428	0.593	0.122	0.953	0.988	0.416
FGF7	0.004	0.003	0.062	0.020	0.017	0.227
IGFBP1	0.654	0.729	0.488	0.999	0.998	0.943
IGFBP2	0.339	0.590	0.428	0.883	0.987	0.902