Figure 5

Network visualization and topology. A. Part of the core sub network derived from PRIN, and visualized by Cytoscape. B. Insight view of PRIN. Proteins were mapped to 4 subcellular localization: nucleus (blue), mitochondria (cyan), chloroplast (green) and Cytoplasm (pink). Edge colors correspond to co-expression level, and size of nodes corresponds to node degree. C. 7 kinds of hubs were cataloged in our network, partly reference to Jane etal's study [36]. Apart from self-interacted proteins, proteins in PRIN mainly fall into mini hubs, small hubs and medium hubs. D. The shortest path length of PRIN has an aggregation between 2 and 4, showing significant small world properties. E. The node degree distribution of our network shows the scale-free network topological property. F. The high clustering coefficient value indicates that rice protein-protein interaction is highly modular. G. The stress centrality distribution of PRIN implies a strong fault tolerance. H. The first increased followed by a decrease trend in the neighborhood connectivity distribution suggests that it is more prevail that proteins in high degrees interact with low degree proteins in PRIN.