Abstract
Our aim is to build a set of rules, such that reasoning over temporal dependencies within gene regulatory networks is possible. The underlying transitions may be obtained by discretizing observed time series, or they are generated based on existing knowledge, e.g. by Boolean networks or their nondeterministic generalization. We use the mathematical discipline of formal concept analysis (FCA), which has been applied successfully in domains as knowledge representation, data mining or software engineering. By the attribute exploration algorithm, an expert or a supporting computer program is enabled to decide about the validity of a minimal set of implications and thus to construct a sound and complete knowledge base. From this all valid implications are derivable that relate to the selected properties of a set of genes. We present results of our method for the initiation of sporulation in Bacillus subtilis. However the formal structures are exhibited in a most general manner. Therefore the approach may be adapted to signal transduction or metabolic networks, as well as to discrete temporal transitions in many biological and nonbiological areas.
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.
Similar content being viewed by others
References
Chabrier-Rivier, N., et al.: Modeling and Querying Biomolecular Interaction Networks. Theor. Comp. Sc. 325(1), 25–44 (2004)
Choi, V., et al.: Using Formal Concept Analysis for Microarray Data Comparison. Advances in Bioinformatics and Computational Biology 5, 57–66 (2006)
Ganter, B., Stumme, G., Wille, R. (eds.): Formal Concept Analysis. LNCS (LNAI), vol. 3626. Springer, Heidelberg (2005)
Ganter, B., Wille, R.: Formal Concept Analysis - Mathematical Foundations. Springer, Heidelberg (1999)
de Jong, H., et al.: Qualitative Simulation of the Initiation of Sporulation in Bacillus subtilis. Bulletin of Mathematical Biology 66, 261–299 (2004)
Esparza, J.: Model checking using net unfoldings. Sci. Comput. Programm 23, 151–195 (1994)
von Hentig, H.: Magier oder Magister? Über die Einheit der Wissenschaft im Verständigungsprozess. Suhrkamp, Frankfurt (1974)
Kauffman, S.A.: The Origins of Order: Self-Organization and Selection in Evolution. Oxford University Press, New York (1993)
Klamt, S., et al.: A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics 7(56) (2006)
Kuznetsov, S.O., Obiedkov, S.A.: Counting Pseudo-intents and #P-completeness. In: Missaoui, R., Schmidt, J. (eds.) ICFCA 2006. LNCS (LNAI), vol. 3874, pp. 306–308. Springer, Heidelberg (2006)
King, R.D., Garrett, S.W., Coghill, G.M.: On the Use of Qualitative Reasoning to Simulate and Identify Metabolic Pathways. Bioinformatics 21(9), 2017–2026 (2005)
Laubenbacher, R.: Algebraic Models in Systems Biology. In: Anai, H., Horimoto, K. (eds.) Algebraic Biology 2005, pp. 33–35. Universal Academy Press, Tokyo (2005)
Motameny, S., Versmold, B., Schmutzler, R.: Formal Concept Analysis for the Identification of Combinatorial Biomarkers in Breast Cancer. In: Medina, R., Obiedkov, S.A. (eds.) ICFCA 2008. LNCS, vol. 4933, pp. 229–240. Springer, Heidelberg (2008)
Peirce, C.S.: How to Make Our Ideas Clear. In: Hartshorne, C., Weiss, P. (eds.) Collected papers. Harvard University Press, Cambridge/Mass (1931-1935)
Ganter, B., Rudolph, S.: Formal Concept Analysis Methods for Dynamic Conceptual Graphs. In: Delugach, H.S., Stumme, G. (eds.) ICCS 2001. LNCS (LNAI), vol. 2120, pp. 143–156. Springer, Heidelberg (2001)
Steggles, L.J., et al.: Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach. Bioinformatics 23(3), 336–343 (2007)
Tomas, C.A., et al.: DNA array-based transcriptional analysis of asporogenous, nonsolventogenic Clostridium acetobutylicum strains SKO1 and M5. J. Bacteriol. 15, 4539–4547 (2003)
Wollbold, J.: Attribute Exploration of Discrete Temporal Transitions. In: Gély, A., et al. (eds.) ICFCA 2007, Clermont-Ferrand, pp. 121–130 (2007)
Wollbold, J., Huber, R., Wolff, K.E.: Conceptual Representation of Gene Expression Processes. In: Knowledge Processing in Practice 2007. LNCS (LNAI). Springer, Heidelberg (to appear, 2008)
Zickwolff, M.: Rule Exploration: First Order Logic in Formal Concept Analysis. PhD thesis. University of Technology, Darmstadt (1991)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Wollbold, J., Guthke, R., Ganter, B. (2008). Constructing a Knowledge Base for Gene Regulatory Dynamics by Formal Concept Analysis Methods. In: Horimoto, K., Regensburger, G., Rosenkranz, M., Yoshida, H. (eds) Algebraic Biology. AB 2008. Lecture Notes in Computer Science, vol 5147. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-85101-1_17
Download citation
DOI: https://doi.org/10.1007/978-3-540-85101-1_17
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-85100-4
Online ISBN: 978-3-540-85101-1
eBook Packages: Computer ScienceComputer Science (R0)