Abstract
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.
This work was supported by the Ministry of Information and Communication of Korea under grant number IMT2000-C3-4.
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© 2003 Springer-Verlag Berlin Heidelberg
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Byun, Y., Han, K. (2003). Visualization of Protein-Protein Interaction Networks Using Force-Directed Layout. In: Sloot, P.M.A., Abramson, D., Bogdanov, A.V., Gorbachev, Y.E., Dongarra, J.J., Zomaya, A.Y. (eds) Computational Science — ICCS 2003. ICCS 2003. Lecture Notes in Computer Science, vol 2659. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44863-2_20
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DOI: https://doi.org/10.1007/3-540-44863-2_20
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