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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Online Animated Graph Drawing for Web Navigation. Springer, London (1997)
A Fully Animated Interactive System for Clustering and Navigating Huge Graphs. Springer, London (1998)
Expression system - definition. Biology Online. Biology-Online.org., 10 (2005)
Integration of biological networks and gene expression data using cytoscape (2007)
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)
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)
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)
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)
Bairoch, A.: The ENZYME database in 2000. Nucl. Acids Res. 28(1), 304–305 (2000)
Benno, S., Peter, U., Stanley, F.: A network of protein-protein interactions in yeast. Nature Biotechnology 18, 1257–1261 (2000)
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
Burnett, G., Kennedy, E.P.: The Enzymatic Phosphorylation of Proteins. J. Biol. Chem. 211(2), 969–980 (1954)
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)
Kaissi, M.E., Dickerson, J., Wuertele, E., Reiners, D.: Mnv: Metabolic twork visualization.
El Kaissi, M., Dickerson, J., Wuertele, E., Reiners, D.: Reaction centric layout for metabolic networks. LNCS. Springer, Heidelberg (2009)
Ellson, J., Gansner, E., Koutsofios, L., North, S., Woodhull, G.: Graphviz open source graph drawing tools (2002)
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)
Friedrich, C., Schreiber: Visualisation and navigation methods for typed protein-protein interaction networks. Applied bioinformatics 2(3 suppl.) (2003)
Friedrich, C., Houle, M.: Graph drawing in motion ii., pp. 122–125 (2002)
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)
Kauffman, S.A.: The Origins of Order: Self-Organization and Selection in Evolution. Oxford University Press, Oxford (1993)
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)
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)
Museth, K., Möller, T., Ynnerman, A.: In: Archambault, D., Munzner, T., Auber, D. (eds.) Grouse: Feature-based, steerable graph hierarchy exploration (2007)
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)
Supratim, C.: Gene regulation and molecular toxicology. Toxicology Mechanisms and Methods 15, 1–23 (2004)
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)
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)
Vidal, M.: A biological atlas of functional maps. Cell 104(3), 333–339 (2001)
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)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights 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). Visualization of Gene Regulatory 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_87
Download citation
DOI: https://doi.org/10.1007/978-3-642-10520-3_87
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)