Human Protein Protein Interaction Networks: A Topological Comparison Review

TL;DR

This paper compares four human protein-protein interaction networks topologically, revealing shared genes but significant differences in interactions and roles, especially within cancer-related sub-networks, impacting their use in biological studies.

Contribution

It provides a comprehensive topological comparison of human protein networks, highlighting their similarities and differences for better application in biomedical research.

Findings

Networks share common genes but differ in interactions

Cancer pathway sub-networks show higher topological consistency

Genes have different roles across networks

Abstract

Protein-Protein Interaction Networks aim to model the interactome, providing a powerful tool for understanding the complex relationships governing cellular processes. These networks have numerous applications, including functional enrichment, discovering cancer driver genes, identifying drug targets, and more. Various databases make protein-protein networks available for many species, including Homo sapiens. This work topologically compares four Homo sapiens networks using a coarse-to-fine approach, comparing global characteristics, sub-network topology, specific nodes centrality, and interaction significance. Results show that the four human protein networks share many common protein-encoding genes and some global measures, but significantly differ in the interactions and neighbourhood. Small sub-networks from cancer pathways performed better than the whole networks, indicating an improved topological consistency in functional pathways. The centrality analysis shows that the same genes play different roles in different networks. We discuss how studies and analyses that rely on protein-protein networks for humans should consider their similarities and distinctions.