caa a22 4500 445843004 CHVBK 20180317145350.0 cr unu---uuuuu 170323e20110601xx s 000 0 eng 10.1007/s11047-010-9178-0 doi (NATIONALLICENCE)springer-10.1007/s11047-010-9178-0 Petri net representation of multi-valued logical regulatory graphs [Elektronische Daten] [C. Chaouiya, A. Naldi, E. Remy, D. Thieffry] Relying on a convenient logical representation of regulatory networks, we propose a generic method to qualitatively model regulatory interactions in the standard elementary and coloured Petri net frameworks. Logical functions governing the behaviours of the components of logical regulatory graphs are efficiently represented by Multivalued Decision Diagrams, which are also at the basis of the translation of logical models in terms of Petri nets. We further delineate a simple strategy to sort trajectories through the introduction of priority classes (in the logical framework) or priority functions (in the Petri net framework). We also focus on qualitative behaviours such as multistationarity or sustained oscillations, identified as specific structures in state transition graphs (for logical models) or in marking graphs (in Petri nets). Regulatory circuits are known to be at the origin of such properties. In this respect, we present a method that allows to determine the functionality contexts of regulatory circuits, i.e. constraints on external regulator states enabling the corresponding dynamical properties. Finally, this approach is illustrated through an application to the modelling of a regulatory network controlling T lymphocyte activation and differentiation. Springer Science+Business Media B.V., 2010 Gene regulation nationallicence Biological networks nationallicence Regulatory circuits nationallicence Logical modelling nationallicence Petri nets nationallicence Signal transduction nationallicence Cell differentiation nationallicence Chaouiya C. Instituto Gulbenkian de Ciência, Oeiras, Portugal aut Naldi A. INSERM U928—TAGC, Marseille, France aut Remy E. Institut de Mathématiques de Luminy, Marseille, France aut Thieffry D. INSERM U928—TAGC, Marseille, France aut Natural Computing Springer Netherlands 10/2(2011-06-01), 727-750 1567-7818 10:2<727 2011 10 11047 https://doi.org/10.1007/s11047-010-9178-0 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s11047-010-9178-0 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Chaouiya C. Instituto Gulbenkian de Ciência, Oeiras, Portugal aut NATIONALLICENCE 700 1- Naldi A. INSERM U928—TAGC, Marseille, France aut NATIONALLICENCE 700 1- Remy E. Institut de Mathématiques de Luminy, Marseille, France aut NATIONALLICENCE 700 1- Thieffry D. INSERM U928—TAGC, Marseille, France aut NATIONALLICENCE 773 0- Natural Computing Springer Netherlands 10/2(2011-06-01), 727-750 1567-7818 10:2<727 2011 10 11047 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer