TY - JOUR
T1 - Computing Signal Transduction in Signaling Networks modeled as Boolean Networks, Petri Nets, and Hypergraphs
JF - bioRxiv
DO - 10.1101/272344
SP - 272344
AU - Luis Sordo Vieira
AU - Paola Vera-Licona
Y1 - 2019/01/01
UR - http://biorxiv.org/content/early/2019/06/02/272344.abstract
N2 - Mathematical frameworks circumventing the need of mechanistic detail to build models of signal transduction networks include graphs, hypergraphs, Boolean Networks, and Petri Nets. Predicting how a signal transduces in a signaling network is essential to understand cellular functions and disease. Different formalisms exist to describe how a signal transduces in a given intracellular signaling network represented in the aforementioned modeling frameworks: elementary signaling modes, T-invariants, extreme pathway analysis, elementary flux modes, and simple paths. How do these formalisms compare?We present an overview of how signal transduction networks have been modelled using graphs, hypergraphs, Boolean Networks, and Petri Nets in the literature. We provide a review of the different formalisms for capturing signal transduction in a given model of an intracellular signaling network. We also discuss the existing translations between the different modeling frameworks, and the relationships between their corresponding signal transduction representations that have been described in the literature. Furthermore, as a new formalism of signal transduction, we show how minimal functional routes proposed for signaling networks modeled as Boolean Networks can be captured by computing topological factories, a methodology found in the metabolic networks literature. We further show that in the case of signaling networks represented with an acyclic B-hypergraph structure, the definitions are equivalent. In signaling networks represented as directed graphs, it has been shown that computations of elementary modes via its incidence matrix correspond to computations of simple paths and feedback loops. We show that computing elementary modes based on the incidence matrix of a B-hypergraph fails to capture minimal functional routes.MPSMinimal Path SetEMTEpithelial to Mesenchymal transitionMFRMinimal Functional RouteESMElementary Signaling ModeS-factoryStoichiometric factoryT-factoryTopological factorySF (TF)Stoichiometric (Topological) factoryMSF (MTF)Minimal SF (TF)T-invariantTransition invariantP-invariantPlace invariantsccStrongly Connected ComponentEGFREpidermal Growth Factor ReceptorTGFBRTransforming Growth Factor Beta Receptor IFGFR3Fibroblat Growth Factor Receptor 3MDM2Mouse double minute 2 homolog
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