Visualizing Related Metabolic Pathways in Two and a Half Dimensions (Long Paper)

Brandes, Ulrik and Dwyer, Tim and Schreiber, Falk (2004) Visualizing Related Metabolic Pathways in Two and a Half Dimensions (Long Paper). In: Graph Drawing 11th International Symposium, GD 2003, September 21-24, 2003, Perugia, Italy , pp. 111-122 (Official URL: http://dx.doi.org/10.1007/978-3-540-24595-7_10).

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Abstract

We propose a method for visualizing a set of related metabolic pathways using 2 1/2 D graph drawing. Interdependent, two-dimensional layouts of each pathway are stacked on top of each other so that biologists get a full picture of subtle and significant differences among the pathways. Layouts are determined by a global layout of the union of all pathway-representing graphs using a variant of the proven Sugiyama approach for layered graph drawing that allows edges to cross if they appear in different graphs.

Item Type:Conference Paper
Additional Information:10.1007/978-3-540-24595-7_10
Classifications:S Software and Systems > S.120 Visualization
ID Code:437

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References

F. Alizadeh, R. M. Karp, D.K. Weisser, and G. Zweig. Physical mapping of chromosomes using unique probes. Proceedings of the 5th ACM_SIAM Symposium on Discrete Algorithms (SODA '94), pages 489-500, 1994.

M. Y. Becker and I. Rojas. A graph layout algorithm for drawing metabolic pathways. Bioinformatics, 17(5):461, 2001.

K. S. Booth and G. S. Lueker. Testing for the consecutive ones property, interval graphs, and graph planarity using PQ-tree algorithms. Journal of Computer and System Science, 13(3):335-379, 1976.

U. Brandes and S. R. Corman. Visual unrolling of network evolution and the analysis of dynamic discourse. Proceedings of the IEEE Symposium on Information Visualization 2002 (Info Vis '02), pages 145-151, 2002.

U. Brandes and T. Willhalm. Visualization of bibliographic networks with a reshaped landscape metaphor. Proceedings of the 4th Joint Eurographics and IEEE TCVG Symposium on Visualization (VisSym'02), pages 159-164.ACM, 2002.

T. Dandekar, S. Schuster, B. Snel, M. Huynen, and P. Bork. Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochemical Journal, 343:115-124, 1999.

T. Dwyer and P. Eades. Visualising a fund manager flow graph with columns and worms. Proceedings of the 6th International Conference on Information Visualisation (IV '02), pages 147-152. IEEE Computer Society Press, 2002.

T. Dwyer and P. Eckersley. The WilmaScope 3D graph drawing system. In P. Mutzel and M. Jünger, editors, Graph Drawing Software, Mathematics and Visualization. Springer, 2003.

P. Eades and Q. Feng. Multilevel visualization of clustered graphs. Proceedings of the 4th International Symposium on Graph Drawing (GD '96), volume 1190 of Lecture Notes in Computer Science, pages 113-128. Springer, 1996.

P. Eades and K. Sugiyama. How to draw a directed graph. Journal of Information Processing, 13:424-437, 1990.

C. V. Forst and K. Schulten. Phylogenetic analysis of metabolic pathways. Journal Molecular Evolution, 52:471-489, 2001.

M. Forster, A. Pick, M. Raitner, F. Schreiber, and F. J. Brandenburg. The system Architecture of the BioPath system. In Silico Biology, 2(3):415-426, 2002.

E. R. Gansner, E. Koutsofios, S. C. North, and K.-P. Vo. A technique for drawing directed graphs. Software Engineering, 19(3):214-230, 1993.

P. W. Goldberg, M. C. Golumbic, H. Kaplan and R. Shamir. Four strikes against physical mapping of DNA. Journal of Computational Biology, 2(1):139-152, 1995.

A. Inselberg and B. Dimsdale. Parallel coordinates: A tool for visualizing multidimensional geometry. Proceedings of the 1st IEEE Conference on Visualization (Vis '90), pages 361-378, 1990.

M. Jünger, E. K. Lee, P. Mutzel, and T. Odenthal. A polyhedral approach to the multi-layer crossing minimization problem. Proceedings of the International Symposium on Graph Drawing, Lecture Notes in Computer Science 1353, pages 13-24. Springer, 1997.

M. Kanehisa and S. Goto. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acid Research, 28(1):27-30, 2000.

D. A. Keim. Designing pixel-oriented visualization techniques: Theory and applications. IEEE Transactions on Visualization and Computer Graphics, 6(1):59-78, 2000.

H. Koike. The role of another spatial dimension in software visualization. ACM Transactions on Information Systems, 11(3):266-286, 1993.

L. Liao, S. Kim, and J.-F. Tomb. Genome comparisons based on profiles of metabolic pathways. Proceedings of the 6th International Conference on Knowledge-Based Intelligent Information and Engineering Systems (KES '02), pages 469-476, 2002.

G. Michal. Biochemical Pathways (Poster). Boehringer Mannheim, Penzberg, 1993.

R. Murgai, M. Fujita, and S. C. Krishman. Data sequencing for minimum-transition transmission. Proceedings of the 9th IFIP International Conference on Very Large Scale Integration (VLSI '97), 1997.

V. N. Reddy, M. L. Mavrovouniotis, and M. N. Liebman. Petri net representations of metabolic pathways. Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology (ISMB '93), pages 328-336, 1993.

F. Schreiber. High quality visualization of biochemical pathways in BioPath. In Silico Biology, 2(2):59-73, 2002.

F. Schreiber. Visual Comparison of Metabolic Pathways. Journal of Visual Languages and Computing, 14(4):327-340, 2003.

H. Shiozawa, K. Okada, and Y. Matsushita. 3D interactive visualization for intercell dependencies of spreadsheets. Proceedings of the IEEE Symposium on Information Visualization (InfoVis '99), pages 79-83, 1999.

M. Sirava, T. Schäfer, M. Eiglsperger, M. Kaufmann, O. Kohlbacher, E. Bornberg Bauer, and H.-P. Lenhof. Bio Miner - modeling, analyzing, and visualizing biochemical pathways and networks. Bioinformatics, 18(Suppl. 2):219-230, 2002.

K. Sugiyama, S. Tagawa, and M. Toda. Methods for visual unmderstanding of hierarchical system structures. IEEE Transactions on Systems, Man and Cybernetics, 11(2):109-125, 1981.

Y. Tohsato, H. Matsuda, and A. Hashimoto. A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy. Proceedings of the 8th International Conference of Intelligent Systems for Molecular Biology (ISMB '00), pages 376-383, 2000.

J. Wen. Exploiting orthogonality in three dimensional graphics for visualizing abstract data. Technical Report CS-95-20, Department of Computer Science, Brown University, 1995. http://www.cs.brown.edu/publications/techreports/reports/CS-95-20.html.