Modeling Transport Regulation in Gene Regulatory Networks

Erika Fox; Bree Cummins; William Duncan; Tomáš Gedeon

doi:10.1007/s11538-022-01035-1

Modeling Transport Regulation in Gene Regulatory Networks

Bull Math Biol. 2022 Jul 13;84(8):89. doi: 10.1007/s11538-022-01035-1.

Authors

Erika Fox¹, Bree Cummins², William Duncan², Tomáš Gedeon³

Affiliations

¹ Department of Mathematics, University of Nevada, Reno, NV, USA.
² Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA.
³ Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA. tgedeon@montana.edu.

PMID: 35831627
DOI: 10.1007/s11538-022-01035-1

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.

Keywords: Cellular transport; Gene regulatory networks; Oscillations.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Gene Expression Regulation
Gene Regulatory Networks*
Mathematical Concepts
Models, Biological
Models, Genetic*

Grants and funding

R01 GM126555/GM/NIGMS NIH HHS/United States