Fig. 1

Multilevel map connecting genes via pathways to hallmarks. a Illustration of the automated process that links genes to pathways and to hallmarks. Left A pathway from the Pathway Interaction Database (PID). All genes marked with an orange star are upstream of the Gene ontology (GO) process “negative regulation of apoptotic process” (red box). (The text of the protein complexes and GO processes are not meant to be readable.) Middle A part of the GO hierarchy. The GO process “negative regulation of apoptotic process” is associated with the more general GO process “regulation of programmed cell death” (blue box), which is representative of the cancer hallmark “resisting cell death.” Right Mapping between each hallmark and one or more general GO terms. b Depiction of the multilevel map, which links 1384 genes to 343 pathways and to 10 hallmarks. c A table indicating the number of genes and pathways linked to each of the 10 hallmarks