A Fast Algorithm for Visualizing and Analyzing Protein-Protein Interactions

초록

Today's high-throughput proteomics techniques such as yeast two-hybrid system have produced a rapidly expanding volume of protein interaction data of an unprecedented scale. Due to the volume of data, a graphical representation of protein-protein interactions has proven to be much easier to understand than a long list of interacting proteins. Protein interactions, when visualized as an undirected graph, often yield a nonplanar, disconnected graph with nodes of a 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 algorithm for drawing large-scale protein interaction networks in three-dimensional space, and have implemented the algorithm in a program called InterViewer. Unique features of {\sc InterViewer} include: (1) it is much faster than other recent implementations of forced-directed drawing algorithms, (2) it can be used not only for visualizing protein interactions but also for analyzing subgraphs interactively, and (3) it provides an integrated framework for querying protein-protein interaction databases and directly visualizes the query results. Comparisons with other force-directed drawing programs showed that {\sc InterViewer} generates clear and aesthetically pleasing drawings of large-scale protein interaction networks and that it is an order of magnitude faster than other force-directed programs. It is being extended to work as a web-based application program supporting both wired and wireless communication. InterViewer is available at http://wilab.inha.ac.kr/protein/.