For each ranked gene under different weighting score matrices, we calculated the q-value of each SNP in the gene from the COGA GWAS data. The results for the ten weighting score matrices were summarized in Additional file 1. For each weighting score matrix, its gene ranking performance was expected to increase by improving the q-values of SNPs mapped in the ranked genes. To quantitatively measure performance and correct for gene size, we conducted 100 simulations, in each of which the same number of genes were randomly chosen from the whole gene set. FDR based q-value analysis was then performed on the GWAS genotyped SNPs that mapped to the randomly chosen genes. The proportion of q-values in each q-value bin (e.g., 0.1-0.2) was calculated and then compared with those from the actual ranked alcohol genes. For the simplicity of comparison, we separated q-values into different bins. The results are shown in Additional file 1.
