In parallel, a pathway analysis is only as good as the functional information underlying its pathway definitions. Prominent pathway annotation databases exhibit diverse features (Table 1; also see the online resource Pathguide [17]). The ideal choice of database depends on several variables and their impact on study goals. For example, freeware databases are commonly used due to their ease of access, transparency of features, and visibility in publications. Commercial databases may require a significant investment; however, they are typically linked to user-friendly statistical analysis software and often include high-quality pathway graphics which can be exported to manuscripts. Investigators should weigh the relative importance of these factors during selection.
