Genomics | Bioinformatics
Automatic inference of regulatory and dynamical properties from incomplete gene interaction and expression data
Fabien Corblin*, Eric Fanchon, Laurent Trilling, Claudine Chaouiya, Denis Thieffry
*Corresponding author: Fabien Corblin
Laboratory of Techniques for Biomedical Engineering and Complexity Management: Informatics, Mathematics and Application, Joseph Fourier University (Grenoble 1), Centre National de la Recherche Scientifique, Grenoble, France
F1000Posters 2012, 3: 303 (poster) [English]
9th International Conference on Information Processing in Cells and Tissues (IPCAT) 2012, 31 Mar - 2 Apr 2012, P000
Relying on a multilevel logical formalism, we propose a computational approach enabling us (i) to check the existence of at least one consistent model, given partial data on the regulatory structure and dynamical properties; and (ii) to infer properties common to all consistent models. To this intent, we have developed a dedicated framework, called SysBiOX, which enables the expression of (partial) biological knowledge, dealing with regulatory interactions and expression data, into ASP (Answer Set Programming) constraints. Rather than enumerating the solutions, these are represented in terms of constraints.
We applied this approach to the regulatory network controlling the earliest steps of Drosophila embryo segmentation, i.e. the gap genes and their cross-regulations, under the additional control of maternal gene products. We obtained a unique minimal regulatory graph and 100 properties over discrete kinetic parameters, common to all the minimal models.
No relevant competing interests disclosed.
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