Schematic overview of the subnetwork identification. Schematic overview of the subnetwork identification. The mRNA expression levels of each gene were overlaid on its corresponding protein in the network and subnetworks whose combined activities across the patients have high perturbation score were searched. An activity level (a
) for a subnetwork M
in jth sample was defined as the mean expression levels with the square-root of the number of participating genes in the denominator. The perturbation score S(M
) for the subnetwork was then calculated as the mean over the standard deviation of the activity levels across patients.