An algorithm for the transformation of the Petri net models of biological signaling networks into influence graphs
Simon Gamache-Poirier1, Alexia Souvane2, William Leclerc2
1Département d'informatique et de génie logiciel, Université Laval, Canada; Centre de recherche CERVO, Université Laval, Canada.
Abstract:
A common depiction for biological signaling networks is the influence graph in which the activation and inhibition effects between molecular species are shown with vertices and arcs connecting them. Another formalism for reaction-based models is the Petri nets which has a graphical representation and a mathematical notation that enables structural analysis and quantitative simulation. In this paper, we present an algorithm based on Petri nets topological features for the transformation of the computational model of a biological signaling network into an annotated influence graph. We also show the transformation of the Petri nets model of the beta-adrenergic receptor activating the PKA-MAPK signaling network into its representation as an influence graph.
More Related Videos
13:34A Combined 3D Tissue Engineered In Vitro/In Silico Lung Tumor Model for Predicting Drug Effectiveness in Specific Mutational Backgrounds
Published on: April 6, 2016
07:28JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
Published on: October 19, 2021
Related Concept Videos
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Signal Flow Graphs
In a signal-flow graph, branches denote the system's transfer functions, while nodes represent the signals. The direction of signal flow is indicated by arrows, with the corresponding...
Interactions Between Signaling Pathways
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
Protein-protein Interfaces
Intracellular Signaling Affects Focal Adhesions
Some...
SFG Algebra
Each node in an SFG corresponds to a variable, and the interactions between nodes are represented by branches with associated gains. When multiple branches lead into a node, the value at that node is the sum of the...
