FUMA uses input GWAS summary statistics to compute gene-based P-values (gene analysis) and gene set P-value (gene set analysis) using the MAGMA35 tool. For gene analysis, the gene-based P-value is computed for protein-coding genes by mapping SNPs to genes if SNPs are located within the genes. For gene set analysis, the gene set P-value is computed using the gene-based P-value for 4728 curated gene sets (including canonical pathways) and 6166 GO terms obtained from MsigDB v5.2. For both analyses, the default MAGMA setting (SNP-wise model for gene analysis and competitive model for gene set analysis) are used, and the Bonferroni correction (gene) or FDR (gene-set) was used to correct for multiple testing. 1000G phase 327 is used as a reference panel to calculate LD across SNPs and genes.
