Human protein interaction networks across tissues and diseases

Abstract

Protein interaction networks are an important framework for studying protein function, cellular processes, and genotype-to-phenotype relationships. While our view of the human interaction network is constantly expanding, less is known about networks that form in biologically important contexts such as within distinct tissues or in disease conditions. Here we review efforts to characterize these networks and to harness them to gain insights into the molecular mechanisms underlying human disease.

Keywords: disease-specific network; gene expression; network perturbation; protein interaction network; tissue-specific network.

Figure 1

Feasible protein interactions change between tissues. All protein interactions (A) and feasible protein interactions that connect “global genes,” which are expressed in all three tissues, with tissue-specific genes that are expressed in one tissue out of adipose (B), or thyroid (C), or muscle (D). Data of the genes expressed per tissue were extracted from GTEx Portal (Mele et al., 2015) and limited to genes with 50 counts and above. Data of protein interactions were extracted using MyProteinNet (Basha et al., 2015) from BioGrid (Chatr-Aryamontri et al., 2015), DIP (Xenarios et al., 2002), IntAct (Kerrien et al., 2012), and MINT (Licata et al., 2012) databases. Only global genes that have tissue-specific interactions in each of the three tissues are shown.