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.

Gu et al. BMC Bioinformatics 2011 12:161   doi:10.1186/1471-2105-12-161
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