Broadly, there are two approaches to pathway-based genomic studies. Candidate pathway analysis is hypothesis-driven: pathways are preselected based on prior knowledge and insight. While the number of candidate pathways may vary with study goals (e.g. different effects may be seen within a large, complex pathway compared to numerous, smaller pathways), this approach is marked by its use of a biologically-targeted subset of genomic data. The other approach, genome-wide pathway analysis (GWPA), interrogates a complete genomic data set through pathways representing an extensive range of biology. Notably, the line between “targeted” and “extensive” biological coverage is not precisely drawn. While methods limited to GWPA have been used on data sets with only 1000 genes (~5% of the total number of human genes) [7], the optimal point of delineation between these two approaches warrants further examination.
