A summary of four basic types of tests identifying functional pathway enrichment of a query gene set. (a) In the classic enrichment test, the significance of genes shared by the query and pathway set is assessed. (b) In a rank-based test, each gene is first ranked by an appropriate score, for example, differential expression. A pathway is significant if the corresponding genes are located near the top or bottom of the list. (c) Local network-based methods consider the known topological information between pathway genes. (d) Global network-based methods consider a genome-scale map of known genetic associations.
Wang et al. Genome Biology 2012 13:R125 doi:10.1186/gb-2012-13-12-r125