Protein Networks as Logic Functions in Development and Cancer
Figure 2
Network decision modules underlying embryonic origin, breast cancer metastasis and mesenchymal transformation of brain tumors.
Expression profiles for each of the three case studies are combined with a network of protein-protein interactions among human transcription factors. Network-guided forests are used to identify key network modules that are most important for correct sample classification (representative modules are shown for each study). Grey edges indicate physical protein-protein interactions, blue edges indicate protein combinations that often co-occur in the same decision trees and are most important for classification (as indicated by the permutation test). Node color indicates protein importance whereas edge width indicates the importance of a protein combination. Each module is assigned a decision tree that specifies the output of the module based on the activity of its genes (see also Figure S1).