Fig. 5. The SNP sets based analysis results of principal component-based logistic regression (PC-LR), PLS logistic regression (PLS-LR) and single-locus logistic regression (LR) on the MIPEP-TNFRSF19 gene region from the non-small cell lung cancer GWAS.

The top plot (A) shows the p-values in −log₁₀(p-value) scale (y-axis) of single-locus LR and SNPs sets based PC-LR over the locations (x-axis) of 21 SNPs. The haplotype block-based SNPs sets are showed as boxes on the top. For PC-LR method, the p-values of all SNPs in the same SNPs set are all denoted by the same p-value of the SNPs set. The bottom plot (B) shows the PLS-LR confidence intervals of standardized coefficients (y-axis) over the locations (x-axis) of 21 SNPs. ★: significant at the level of 1E-6.