Straight-Line Drawings of Protein Interactions
This paper presents the first attempt at automatically generating drawings of protein interaction graphs. Such graphs are large and not necessarily connected. A straight-line drawing method based on the spring embedder metaphor has been found highly suitable for this task. The drawings produced exhibit edge length uniformity, even vertex distribution, and preserve graph topology well. This method is capable of generating both two- and three-dimensional layouts. A preliminary evaluation has been carried out based on a representative collection of interaction graphs.
- W. Basalaj. Incremental multidimensional scaling method for database visualization. In Proc. of Visual Data Exploration and Analysis VI, volume SPIE 3643, pages 149–158, January 1999.Google Scholar
- R. Carey and G. Bell. The Annotated VRML 2.0 Reference Manual. Addison-Wesley Developers Press, Reading, MA, USA, 1997.Google Scholar
- P. Eades et al. Preserving the mental map of a diagram. In COMPUGRAPHICS’ 91, pages 34–43, September 1991.Google Scholar
- K. Eilbeck et al. INTERACT: An object oriented protein-protein interaction database. In Proc. of ISMB (in press), 1999.Google Scholar
- P. D. Karp et al. Ecocyc: Encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res, 27:55, 1999.Google Scholar
- J. B. Kruskal and J. B. Seery. Designing network diagrams. In Proc. of the First General Conference on Social Graphics, pages 22–50, October 1978.Google Scholar