Constructing a Knowledge Base for Gene Regulatory Dynamics by Formal Concept Analysis Methods

Authors:
Johannes Wollbold;Reinhard Guthke;Bernhard Ganter
Affiliations:
Institute of Algebra, University of Technology, Dresden, Germany and Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI) Jena, Germany;Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI) Jena, Germany;Institute of Algebra, University of Technology, Dresden, Germany
Venue:
AB '08 Proceedings of the 3rd international conference on Algebraic Biology
Year:
2008

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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 explorationalgorithm, 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.