An interface (CONTEXTS) that we have developed for the analysis of cancer genome studies at the level of biological networks [122, 151]. The upper panel shows the menus for selecting specific cancer studies, databases for pathway analysis (or set of annotations) and the level of confidence required for the relationships. From the user's requests, the system identifies the pathways or functional classes common to the different cancer studies, and the interface allows the corresponding information to be retrieved. The graph represent various cancer studies (those selected in the 'tumor types' panel are represented by red circles) using the pathways extracted from the Reactome database  as the background (the reference selected in the 'Annotation databases' panel and represented by small triangles). For the selected lung cancer study, the 'Lung tumor mutated genes' panel provides a link to the related genes indicating the database (source) from where the information was extracted. The lower panel represents the information on the pathways selected by the user ('innate immunity signaling') as directly provided by the Reactome database.