Visualization of protein-protein interaction networks using force-directed layout

Protein interactions, when visualized as an undirected graph, often yield a nonplanar, disconnected graph with nodes of wide range of degrees. Many graph-drawing programs are of limited use in visualizing protein interactions, either because they are too slow, or because they produce a cluttered drawing with many edge crossings or a static drawing that is not easy to modify to reflect changes in data. We have developed a new force-directed layout algorithm for drawing protein interactions in three-dimensional space. Our algorithm divides nodes into three groups based on their interacting properties: biconnected subgraph in the center, terminal nodes at the outermost region, and the rest in between them. Experimental results show that our algorithm efficiently generates a clear and aesthetically pleasing drawing of large-scale protein interaction networks and that it is much faster than other force-directed layouts.