Straight-Line Drawings of Protein Interactions

Basalaj, Wojciech and Eilbeck, Karen (1999) Straight-Line Drawings of Protein Interactions. In: Graph Drawing 7th International Symposium, GD’99, September 15-19, 1999, Štirín Castle, Czech Republic , pp. 259-266 (Official URL:

Full text not available from this repository.


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.

Item Type:Conference Paper
Additional Information:10.1007/3-540-46648-7_27
Classifications:P Styles > P.720 Straight-line
P Styles > P.060 3D
M Methods > M.400 Force-directed / Energy-based
S Software and Systems > S.999 Others
ID Code:354

Repository Staff Only: item control page


B. Andalman et al. Design gallery browsers based on 2D and 3D graph drawing (demo). In Proc. of Graph Drawing '97, volume LNCS 1353, pages 322-329, September 1997.

P. L. Bartels et al. A protein linkage map of Escherichia coli bacteriophage - T7. Nature Genetics, 12:72-77, 1996.

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.

G. Di Battista et al. Algorithms for drawing graphs: an annotated bibliography. Computational Geometry: Theory and Applications, 4:235-282, 1994.

F. R. Blattner et al. The complete genome sequence of Escherichia coli K-12. Science, 277:1453-74, 1997.

R. Carey and G. Bell. The Annotated VRML 2.0 Reference Manual. Addison-Wesley Developers Press, Reading, MA, USA, 1997

R. A. Clayton et al. The first genome from the third domain of life. Nature, 387:459-462, 1997.

F. S. Collins et al. New goals for the U. S. Human Genome Project: 1998-2003. Science, 282:682-9, 1998.

T. F. Cox and M. A. A. Cox. Multidimensional Scaling. Chapman & Hall, London, 1994.

P. Eades et al. Preserving the mental map of a diagram. In COMPUGRAPHICS '91, pages 34-43, September 1991.

K. Eilbeck et al. INTERACT: An object oriented protein-protein interaction database. In Proc. of ISMB (in press), 1999.

The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science, 282:2012-8, 1998.

M. Fromont-Racine, J. C. Rain, and P. Legrain. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nature Genetics, 16:277-82, 1997.

A. Goffeau et al. Life with 6000 genes. Science, 274:563-7, 1996.

T. Kamada and S. Kawai. An algorithm for drawing general undirected graphs. Information Processing Letters, 31:7-15, 1989.

P. D. Karp et al. Ecocyc: Encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res, 27:55, 1999.

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.

H. W. Mewes et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Res, 27:44-8, 1999.

M.-A. D. Storey and H. Mueller. Graph layout adjustment strategies. In Proc. of Graph Drawing '95, volume LNCS 1027, pages 487-499, September 1995.