In this work we have considered a total of 3 different PPI networks. Two of these networks are derived from the Pathway Commons (PC) resource (Cerami et al., 2011;Rodchenkov et al., 2020), and represent two different releases (PC1 and PC2v11). The other network is derived from the STRING database v11 (Szklarczyk et al., 2019). Briefly, from PC, we downloaded the human PPI network derived from all sources, subsequently selecting interactions annotated to the following interaction types: interacts-with, reacts-with, in-complex-with, used-to-produce and from the following databases: HPRD, BioGRID, BIND, PID, IntAct, PANTHER, KEGG, Reactome, CORUM, DIP and NetPath (Rodchenkov et al., 2020). We further integrated the resulting network with protein cellular localization **data** from the HPRD (Prasad et al., 2009), annotating each protein to its dominant cellular domain: extracellular, cellular membrane, and intra-cellular. Specifically, we removed interactions involving proteins annotated as extracellular with proteins annotated as intracellular. Finally, for the resulting network we extracted the maximally connected component. Integration with gene expression then proceeds by overlaying expression values over the nodes in the maximally connected subnetwork obtained after integrating the PPI with the genes present in the mRNA expression profile.