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Table 4 Analysis of two-way SNP interaction effects on breast cancer.

From: SNP-SNP interactions in breast cancer susceptibility

Two-way Interactions between polymorphisms Crude P-values Bootstrap frequency of stepwise variable selection* Bootstrap P-values FDR adjusted P-values § FPRP
XPD-[Lys751Gln] and IL10-[G(-1082)A] 0.035 68% 0.001 0.007 0.092
COMT-[Met108/158Val] and CCND1-[Pro241Pro] 0.010 61% 0.002 0.014 0.169
GSTP1-[Ile105Val] and COMT-[Met108/158Val] 0.036 54% 0.001 0.007 0.093
CYP17-[C(518)T] and GADD45-[C(IVS3+168)T] 0.024 53% 0.018 0.062 0.999
BARD1-[Pro24Ser] and ESR1-[Pro325Pro] 0.039 51% ns || ns -
TNFA-[G(-308)A] and p27-[Val109Gly] 0.016 49% 0.025 0.079 0.996
BARD1-[Pro24Ser] and p27-[Val109Gly] 0.021 44% ns ns -
BARD1-[Pro24Ser] and XPD-[Lys751Gln] 0.024 36% 0.002 0.014 0.671
ESR1-[Ser10Ser] and ESR1-[Pro325Pro] 0.028 30% 0.097 ns 0.999
  1. Probability to enter the model in the stepwise multivariable model based on the score statistic in the original data set.
  2. *Proportion of times the interaction is selected by the stepwise multivariable model in the 1,000 bootstrap samples.
  3. P-values estimated by bootstrap analysis in the 1,000 random samples.
  4. §False Discovery Rate (FDR) adjusted P-values.
  5. ||ns: p > 0.10.
  6. False Positive Report Probability