In pathway analysis, gene sets corresponding to biological pathways (Box 1) are tested for significant relationships with a phenotype. Primary data for pathway analysis is commonly sourced from genotyping or gene expression arrays, though in theory any data elements that could be mapped to genes or gene products could be used. Importantly, analyzing genomic data through functionally-derived gene sets can reveal larger effects that are otherwise concealed from gene- or SNP-based (single nucleotide polymorphism) analysis. For example, high-profile studies in breast cancer [4], Crohn’s disease [5], and type 2 diabetes [6] demonstrate that functionally-related genes can collectively influence disease susceptibility, even if individual loci do not exhibit genome-wide significant association. As such, pathway analysis represents a potentially powerful and biologically-oriented bridge between genotypes and phenotypes.
