Modeling Transport Regulation in Gene Regulatory Networks

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Date

2022-07

Journal Title

Journal ISSN

Volume Title

Publisher

Springer Science and Business Media LLC

Abstract

A gene regulatory network summarizes the interactions between a set of genes and regulatory gene products. These interactions include transcriptional regulation, protein activity regulation, and regulation of the transport of proteins between cellular compartments. DSGRN is a network modeling approach that builds on traditions of discrete-time Boolean models and continuous-time switching system models. When all interactions are transcriptional, DSGRN uses a combinatorial approximation to describe the entire range of dynamics that is compatible with network structure. Here we present an extension of the DGSRN approach to transport regulation across a boundary between compartments, such as a cellular membrane. We illustrate our approach by searching a model of the p53-Mdm2 network for the potential to admit two experimentally observed distinct stable periodic cycles.

Description

This version of the article has been accepted for publication, after peer review (when applicable) and is subject to Springer Nature’s AM terms of use, but is not the Version of Record and does not reflect post-acceptance improvements, or any corrections. The Version of Record is available online at: http://dx.doi.org/10.1007/s11538-022-01035-1

Keywords

Gene regulatory networks, cellular transport, oscillations

Citation

Fox, E., Cummins, B., Duncan, W., & Gedeon, T. (2022). Modeling Transport Regulation in Gene Regulatory Networks. Bulletin of Mathematical Biology, 84(8), 1-42.
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