Visualization of Gene Regulatory Networks

  • Muhieddine El Kaissi
  • Ming Jia
  • Dirk Reiners
  • Julie Dickerson
  • Eve Wuertele
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5876)

Abstract

Networks are a useful visualization tool for representing many types of biological data such as gene regulations. In this paper, We will present a novel graph drawing technique for visualizing gene regulatory networks. This technique is based on drawing the shortest paths between genes of interest using breadth-first-search algorithm. By drawing genes of interest and showing their regulatory networks, we were able to clearly understand the interaction between these genes. Visualization of Gene Regulatory Networks considerably reduces the number of displayed nodes and edges. This reduction in nodes and edges depends on the number of genes of interest as well as to the number of interactions between these genes.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Online Animated Graph Drawing for Web Navigation. Springer, London (1997)Google Scholar
  2. 2.
    A Fully Animated Interactive System for Clustering and Navigating Huge Graphs. Springer, London (1998)Google Scholar
  3. 3.
    Expression system - definition. Biology Online. Biology-Online.org., 10 (2005)Google Scholar
  4. 4.
    Integration of biological networks and gene expression data using cytoscape (2007)Google Scholar
  5. 5.
    Abello, J., van Ham, F., Krishnan, N.: Ask-graphview: A large scale graph visualization system. IEEE Transactions on Visualization and Computer Graphics 12(5), 669–676 (2006)CrossRefGoogle Scholar
  6. 6.
    Aryamontri, C.A., Ceol, A., Palazzi, L.M., Nardelli, G., Schneider, M.V., Castagnoli, L., Cesareni, G.: Mint: the molecular interaction database. Nucleic Acids Res. 35(Database issue) (January 2007)Google Scholar
  7. 7.
    Auber, D.: Tulip: A huge graph visualisation framework. In: Mutzel, P., Jünger, M. (eds.) Graph Drawing Softwares. Mathematics and Visualization, pp. 105–126. Springer, Heidelberg (2003)Google Scholar
  8. 8.
    Madan Babu, M., Luscombe, N.M., Aravind, L., Gerstein, M., Teichmann, S.A.: Structure and evolution of transcriptional regulatory networks. Current Opinion in Structural Biology 14(3), 283–291 (2004)CrossRefGoogle Scholar
  9. 9.
    Bairoch, A.: The ENZYME database in 2000. Nucl. Acids Res. 28(1), 304–305 (2000)CrossRefGoogle Scholar
  10. 10.
    Benno, S., Peter, U., Stanley, F.: A network of protein-protein interactions in yeast. Nature Biotechnology 18, 1257–1261 (2000)CrossRefGoogle Scholar
  11. 11.
    Breitkreutz, B.-J., Stark, C., Tyers, M.: Osprey: A network visualization system. Genome Biology 3(12);preprint0012.1–preprint0012.6 (2002); This was the first version of this article to be made available publicly. A peer-reviewed and modified version, http://genomebiology.com/2003/4/3/R22
  12. 12.
    Burnett, G., Kennedy, E.P.: The Enzymatic Phosphorylation of Proteins. J. Biol. Chem. 211(2), 969–980 (1954)Google Scholar
  13. 13.
    Cheadle, C., Fan, J., Cho-Chung, Y., Werner, T., Ray, J., Do, L., Gorospe, M., Becker, K.: Control of gene expression during t cell activation: alternate regulation of mrna transcription and mrna stability. BMC Genomics 6(1), 75 (2005)CrossRefGoogle Scholar
  14. 14.
    Kaissi, M.E., Dickerson, J., Wuertele, E., Reiners, D.: Mnv: Metabolic twork visualization.Google Scholar
  15. 15.
    El Kaissi, M., Dickerson, J., Wuertele, E., Reiners, D.: Reaction centric layout for metabolic networks. LNCS. Springer, Heidelberg (2009)Google Scholar
  16. 16.
    Ellson, J., Gansner, E., Koutsofios, L., North, S., Woodhull, G.: Graphviz open source graph drawing tools (2002)Google Scholar
  17. 17.
    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)CrossRefGoogle Scholar
  18. 18.
    Friedrich, C., Schreiber: Visualisation and navigation methods for typed protein-protein interaction networks. Applied bioinformatics 2(3 suppl.) (2003)Google Scholar
  19. 19.
    Friedrich, C., Houle, M.: Graph drawing in motion ii., pp. 122–125 (2002)Google Scholar
  20. 20.
    Hu, Z., Mellor, J., Wu, J., Yamada, T., Holloway, D., DeLisi, C.: VisANT: data-integrating visual framework for biological networks and modules. Nucl. Acids Res. 33(2), 352–357 (2005)CrossRefGoogle Scholar
  21. 21.
    Kauffman, S.A.: The Origins of Order: Self-Organization and Selection in Evolution. Oxford University Press, Oxford (1993)Google Scholar
  22. 22.
    Lawrence, M., Lee, E.-K., Cook, D., Hofmann, H., Wurtele, E.: explorase: Exploratory data analysis of systems biology data. In: CMV 2006: Proceedings of the Fourth International Conference on Coordinated & Multiple Views in Exploratory Visualization, Washington, DC, USA, pp. 14–20. IEEE Computer Society, Los Alamitos (2006)CrossRefGoogle Scholar
  23. 23.
    Munzner, T.: Drawing large graphs with h3Viewer and site manager. In: Whitesides, S.H. (ed.) GD 1998. LNCS, vol. 1547, pp. 384–393. Springer, Heidelberg (1999)CrossRefGoogle Scholar
  24. 24.
    Museth, K., Möller, T., Ynnerman, A.: In: Archambault, D., Munzner, T., Auber, D. (eds.) Grouse: Feature-based, steerable graph hierarchy exploration (2007)Google Scholar
  25. 25.
    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)CrossRefGoogle Scholar
  26. 26.
    Supratim, C.: Gene regulation and molecular toxicology. Toxicology Mechanisms and Methods 15, 1–23 (2004)CrossRefGoogle Scholar
  27. 27.
    Taylor, R.W., Sarkar, M., Brown, M.H.: Graphical fisheye views of graphs. In: Proceedings of CHI 1992 Conference on Human Factors in Computing Systems, pp. 83–91. ACM Press, New York (1992)Google Scholar
  28. 28.
    van Wijk, J.J., Nuij, W.A.A.: Smooth and efficient zooming and panning. In: IEEE Symposium on Information Visualization (INFOVIS 2003), October, 2003, pp. 15–23 (2003)Google Scholar
  29. 29.
    Vidal, M.: A biological atlas of functional maps. Cell 104(3), 333–339 (2001)CrossRefMathSciNetGoogle Scholar
  30. 30.
    Yu, H., Luscombe, N.M., Lu, H.X., Zhu, X., Xia, Y., Han, J.-D.J., Bertin, N., Chung, S., Vidal, M., Gerstein, M.: Annotation transfer between genomes: Protein protein interologs and protein dna regulogs. Genome Research 14(6), 1107–1118 (2004)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Muhieddine El Kaissi
    • 1
  • Ming Jia
    • 2
  • Dirk Reiners
    • 1
  • Julie Dickerson
    • 2
  • Eve Wuertele
    • 2
  1. 1.CACSUniversity of LouisianaLafayette
  2. 2.VRACIowa State UniversityAmes

Personalised recommendations