1. A method for visualizing large-scale protein interaction data, which yields a three-dimensional graph using proteins as nodes and interactions between the proteins as edges, comprising the steps of: producing an initial layout by placing all nodes of protein interaction data on the surface of a sphere by increasing horizontal and vertical angles of polar coordinates; and yielding a graph by iterating a process moving each node of the initial layout to an equilibrium position considering global spring forces between non-adjacent nodes as well as local spring forces between adjacent nodes, on a predetermined number of times.