Skip to main content

Reaction Centric Layout for Metabolic Networks

  • Conference paper
Advances in Visual Computing (ISVC 2009)

Part of the book series: Lecture Notes in Computer Science ((LNIP,volume 5876))

Included in the following conference series:

Abstract

The challenge is to understand and visualize large networks with many elements while at the same time give the biologist enough of an overview of the whole network to see and understand relationships between subnets. Classical biological visualization systems like Cytoscape use standard graph layout algorithms based on the molecules (DNA, RNA, proteins, metabolites) involved in the processes. We propose a new approach that instead focuses on the reactions that transform molecules, using higher-level macro-glyphs that summarize a large number of molecules in a compact unit, thus forming very natural and automatic clusters. We also employ natural clustering approaches to other areas of typical metabolic networks. The result is a graph with about 50-60% of the original node and 20-30% of the original edge count, which simplifies efficient layout and interaction significantly.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  1. A History of Molecular Biology. Harvard University Press, Cambridge (2000)

    Google Scholar 

  2. Auber, D.: Exploring InfoVis Publication History with Tulip. In: Mutzel, P., Jünger, M. (eds.) Graph Drawing Softwares, Mathematics and Visualization, pp. 10–126. Springer, Heidelberg (2004)

    Google Scholar 

  3. Bourqui, R., Auber, D., Lacroix, V., Jourdan, F.: Metabolic network visualization using constraint planar graph drawing algorithm. In: IV 2006: Proceedings of the conference on Information Visualization, Washington, DC, USA, pp. 489–496. IEEE Computer Society Press, Los Alamitos (2006)

    Google Scholar 

  4. Bourqui, R., Cottret, L., Lacroix, V., Auber, D., Mary, P., Sagot, M.-F., Jourdan, F.: Metabolic network visualization eliminating node redundance and preserving metabolic pathways. BMC Systems Biology 1(1), 29 (2007)

    Article  Google Scholar 

  5. Dogrusoz, U., Erson, E.Z., Giral, E., Demir, E., Babur, O., Cetintas, A., Colak, R.: PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization. Bioinformatics 22(3), 374–375 (2006)

    Article  Google Scholar 

  6. Kaissi, M.E., Dickerson, J., Wuertele, E., Reiners, D.: Mnv: Metabolic network visualization

    Google Scholar 

  7. Kaissi, M.E., Dickerson, J., Wuertele, E., Reiners, D.: Visualization of gene regulatory networks. LNCS. Springer, Heidelberg (2009)

    Google Scholar 

  8. Ellson, J., Gansner, E., Koutsofios, L., North, S., Woodhull, G.: Graphviz open source graph drawing tools (2002)

    Google Scholar 

  9. Enright, A.J., Ouzounis, C.A.: Biolayout–an automatic graph layout algorithm for similarity visualization. Bioinformatics 17(9), 853–854 (2001)

    Article  Google Scholar 

  10. Wurtele, E.S., Li, L., Berleant, D., Cook, D., Dickerson, J.A., Ding, J., Hofmann, H., Lawrence, M., Lee, E.K., Li, J., Mentzen, W., Miller, L., Nikolau, B.J., Ransom, N., Wang, Y.: Metnet: Software to build and model the biogenetic lattice of arabidopsis. In: Concepts in Plant Metabolomics, pp. 145–158. Springer, Heidelberg (2007)

    Chapter  Google Scholar 

  11. Fruchtermanand, T.M.J., Reingold, E.M.: Graph drawing by force-directed placement. Softw. Pract. Exper. 21(11), 1129–1164 (1991)

    Article  Google Scholar 

  12. Funahashi, A., Morohashi, M., Kitano, H., Tanimura, N.: Celldesigner: a process diagram editor for gene-regulatory and biochemical networks. BIOSILICO 1(5), 159–162 (2003)

    Article  Google Scholar 

  13. Tamassia, R., di Battista, G., Eades, P., Tollis, I.G.: Graph Drawing:Algorithms for the Visualization of Graphs. Prentice-Hall, Englewood Cliffs (1999)

    MATH  Google Scholar 

  14. Guo, H., Ecker, J.R.: The ethylene signaling pathway: new insights. Current Opinion in Plant Biology 7(1), 40–49 (2004)

    Article  Google Scholar 

  15. Iragne, F., Nikolski, M., Mathieu, B., Auber, D., Sherman, D.: ProViz: protein interaction visualization and exploration. Bioinformatics 21(2), 272–274 (2005)

    Article  Google Scholar 

  16. Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., Ideker, T.: Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Research 13(11), 2498–2504 (2003)

    Article  Google Scholar 

  17. Suderman, M., Hallett, M.: Tools for visually exploring biological networks. Bioinformatics 23(20), 2651–2659 (2007)

    Article  Google Scholar 

  18. Shinfuku, Y., Ono, N., Hogiria, T., Furusawa, C., Shimizu, H.: Analysis of metabolic network based on conservation of molecular structure. Biosystems 95(3), 175–178 (2008)

    Google Scholar 

  19. Yang, Y., Engin, L., Wurtele, E.S., Cruz-Neira, C., Dickerson, J.A.: Integration of metabolic networks and gene expression in virtual reality. Bioinformatics 21(18), 3645–3650 (2005)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

El Kaissi, M., Jia, M., Reiners, D., Dickerson, J., Wuertele, E. (2009). Reaction Centric Layout for Metabolic Networks. In: Bebis, G., et al. Advances in Visual Computing. ISVC 2009. Lecture Notes in Computer Science, vol 5876. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-10520-3_8

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-10520-3_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-10519-7

  • Online ISBN: 978-3-642-10520-3

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics