Chunk #58 — Materials and Methods — Meta-Analysis Gene-set Enrichment of variaNT Associations (MAGENTA) — Step 4: Gene set enrichment analysis of genome-wide association data
The specific steps of the GSEA statistical test employed here are as follows: (i) Corrected gene association p-values were calculated for all genes in the genome, based on a given GWA study or meta-analysis. In this study, we used the corrected gene p-value, as it can be computed for studies where individuals' genotypes are not available. If genotype data are available, the gene score can also be computed (see above for definition and section below for definition). (ii) Several types of genes were removed from gene sets. Genes with no SNPs in their extended gene boundaries were not included in the analysis. In addition, for each subset of genes in a given gene set that were assigned the same most significant SNP, all genes but one were removed from the analysis; the gene with the most significant gene score was retained. This was done to eliminate potential inflation of gene set enrichment significance due to two or more genes in a gene set that are physically proximal along the chromosome and hence may capture the same association signal (assuming one
