Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: Large‐scale organization and robustness

Abstract

High-throughput screens have begun to reveal protein interaction networks in several organisms. To understand the general properties of these protein interaction networks, a systematic analysis of topological structure and robustness was performed on the protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster. It shows that the three protein interaction networks have a scale-free and high-degree clustering nature as the consequence of their hierarchical organization. It also shows that they have the small-world property with similar diameter at 4-5. Evaluation of the consequences of random removal of both proteins and interactions from the protein interaction networks suggests their high degree of robustness. Simulation of a protein's removal shows that the protein interaction network's error tolerance is accompanied by attack vulnerability. These fundamental analyses of the networks might serve as a starting point for further exploring complex biological networks and the coming research of "systems biology".

A Systemic Network for Chlamydia pneumoniae Entry into Human Cells

“…Network hubs are likely to play essential roles in the biological networks (5,26,41,48). Hubs are nodes with high connectivity to other nodes and can be identified via examining their contributions to network interconnectivity and diameter.…”

Integrated Systems View on Networking by Hormones in Arabidopsis Immunity Reveals Multiple Crosstalk for Cytokinin

“…Based on the type of interacting nodes, the following networks can be distinguished: metabolic (Schuster et al, 2000), protein-protein interaction (Li et al, 2006), transcriptional regulation (Sato et al, 2010), and signaling networks (Liu et al, 2010). Depending upon the network, edges are either nondirectional or directed from one node to the other.…”

A New Approach to Find Orthologous Proteins Using Sequence and Protein-Protein Interaction Similarity

“…Although sequence similarity decides the first ortholog candidate in Ideker's system and OrthoInterBlast, sequence score also contributes to the final decision of the ortholog in OrthoInterBlast. It is because we want to reduce the effect of false positive interaction data (Li et al, 2006).…”