Gene-based test/gene-set analyses are methods that enable to summarize SNP associations at the gene level and associate the set of genes to biological pathways. For instance, VEGAS performs permutation based simulation33,34, MAGMA employs multiple linear regression35 and Pascal computes sum and maximum of chi-squared statistics36 to obtain gene-based P-values. Additionally, there are several tools that perform not only gene-based test but also gene-set analyses using full distribution of genetic associations (e.g., MAGMA35, MAGENTA37, INRICH38, and DEPICT39). FUMA implements MAGMA gene-based analysis and gene-set analysis on the full GWAS input data. In addition, genes prioritized by SNP2GENE or by the user are also tested for overrepresentation in various gene sets in GENE2FUNC process.
