A Layout Algorithm for Signaling Pathways

Genc, B and Dogrusoz, U (2006) A Layout Algorithm for Signaling Pathways. [Journal (On-line/Unpaginated)]

Full text not available from this repository.

Abstract

Visualization is crucial to the effective analysis of biological pathways. A poorly laid out pathway confuses the user, while a well laid out one improves the user’s comprehension of the underlying biological phenomenon. We present a new, elegant algorithm for layout of biological signaling pathways. Our algorithm uses a force-directed layout scheme, taking into account directional and rectangular regional constraints enforced by different molecular interaction types and subcellular locations in a cell. The algorithm has been successfully implemented as part of a pathway visualization and analysis toolkit named Patika, and results with respect to computational complexity and quality of the layout have been found satisfactory. The algorithm may be easily adapted to be used in other applications with similar conventions and constraints as well. Patika version 1.0 beta is available upon request at http://www.patika.org.

Item Type:Journal (On-line/Unpaginated)
Additional Information:10.1016/j.ins.2004.11.006
Keywords:Bioinformatics; Signaling pathways; Cellular pathway analysis; pathway visualization
Classifications:S Software and Systems > S.001 General
M Methods > M.400 Force-directed / Energy-based
G Algorithms and Complexity > G.001 General
ID Code:739

Repository Staff Only: item control page

References

G. Di Battista, P. Eades, R. Tamassia, I.G. Tollis, Graph Drawing, Algorithms for the Visualization of Graphs, Prentice-Hall, 1999.

U. Dogrusoz, Q. Feng, B. Madden, M. Doorley, A. Frick, Graph visualization toolkits, IEEE Computer Graphics and Applications 22 (1) (2002) 30–37.

M. Arnone, E. Davidson, The hardwiring of development: organization and function of genomic regulatory systems, Development 124 (10) (1997) 1851–1864.

G. Miklos, G. Rubin, The role of the genome project in determining gene function: insights from model organisms, Cell 86 (4) (1996) 521–529.

H. Ogata, S. Goto, K. Sato, W. Fujibuchi, H. Bono, M. Kanehisa, KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleid Acids Research 27 (1999) 29–34, Available from <http://www.genome.ad.jp/kegg/>.

P. Karp, M. Riley, M. Saier, I. Paulsen, J. Collado-Vides, S. Paley, A. Pellegrini-Toole, C. Bonavides, S. Gama-Castro, The EcoCyc database, Nucleic Acids Research 30 (1) (2002) 56–58.

WIT, What is there? Interactive Metabolic Reconstruction on the Web, Available from <http://wit.mcs.anl.gov> 2001.

E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, G. Nisanci, R. Cetin-Atalay, M. Ozturk, PATIKA: An integrated visual environment for collaborative construction and analysis of cellular pathways, Bioinformatics 18 (7) (2002) 996–1003.

E. Wingender, X. Chen, The TRANSFAC system on gene expression regulation, Nucleic Acids Research 29 (1) (2001) 281–283.

T. Takai-Igarashi, T. Kaminuma, A pathway finding system for the cell signaling networks database, In Silico Biology 1 (1999) 129–146.

T. Kamps, J. Kleinz, Constraint-based spring-model algorithm for graph layout, in: F. Brandenburg (Ed.), Graph Drawing (Proc. GD Õ95), Lecture Notes in Computer Science, vol. 1027, Springer-Verlag, 1995, pp. 349–360.

T. Lin, P. Eades, Integration of declarative and algorithmic approaches for layout creation, in: R. Tamassia, I. Tollis (Eds.), Graph Drawing (Proc. GD Õ94), Lecture Notes in Computer Science, vol. 894, Springer-Verlag, 1995, pp. 376–387.

X. Wang, I. Miyamoto, Generating customized layouts, in: F. Brandenburg (Ed.), Graph Drawing (Proc. GD Õ95), Lecture Notes in Computer Science, vol. 1027, Springer-Verlag, 1995, pp. 504–515.

W. He, K. Marriott, Constrained graph layout, in: S. North (Ed.), Graph Drawing (Proc. GD Ö96), Lecture Notes in Computer Science, vol. 1190, Springer-Verlag, 1997, pp. 217–232.

P.D. Karp, S. Paley, Automated drawing of metabolic pathways, in: Third International Conference on Bioinformatics and Genome Research, Tallahassee, FL, 1994, pp. 225–238.

M.Y. Becker, I. Rojas, A graph layout algorithm for drawing metabolic pathways, Bioinformatics 17 (2001) 461–467.

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

K. Sugiyama, S. Tagawa, M. Toda, Methods for visual understanding of hierarchical systems, IEEE Transactions on Systems, Man, and Cybernetics 21 (2) (1981) 109–125.

E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, A. Ayaz, G. Gulesir, G. Nisanci, R. Cetin-Atalay, An ontology for collaborative construction and analysis of cellular pathways, Bioinformatics 20 (3) (2004) 349–356.

T.M.J. Fruchterman, E.M. Reingold, Graph drawing by force-directed placement, Software Practice and Experience 21 (11) (1991) 1129–1164.

K. Sugiyama, K. Misue, A simle and unified method for drawing graphs: Magnetic-spring algorithm, in: R. Tamassia, I. Tollis (Eds.), Graph Drawing (Proc. GD Õ94), Lecture Notes in Computer Science, vol. 894, Springer-Verlag, 1995, pp. 364–375.