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Analysis of gene network robustness based on saturated fixed point attractors

Author(s): Li, Genyuan; Rabitz, Herschel

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dc.contributor.authorLi, Genyuan-
dc.contributor.authorRabitz, Herschel-
dc.date.accessioned2020-10-30T18:35:17Z-
dc.date.available2020-10-30T18:35:17Z-
dc.date.issued2014-12en_US
dc.identifier.citationLi, Genyuan, Rabitz, Herschel. (2014). Analysis of gene network robustness based on saturated fixed point attractors. EURASIP Journal on Bioinformatics and Systems Biology, 2014 (1), 10.1186/1687-4153-2014-4en_US
dc.identifier.urihttp://arks.princeton.edu/ark:/88435/pr1g51v-
dc.description.abstractThe analysis of gene network robustness to noise and mutation is important for fundamental and practical reasons. Robustness refers to the stability of the equilibrium expression state of a gene network to variations of the initial expression state and network topology. Numerical simulation of these variations is commonly used for the assessment of robustness. Since there exists a great number of possible gene network topologies and initial states, even millions of simulations may be still too small to give reliable results. When the initial and equilibrium expression states are restricted to being saturated (i.e., their elements can only take values 1 or −1 corresponding to maximum activation and maximum repression of genes), an analytical gene network robustness assessment is possible. We present this analytical treatment based on determination of the saturated fixed point attractors for sigmoidal function models. The analysis can determine (a) for a given network, which and how many saturated equilibrium states exist and which and how many saturated initial states converge to each of these saturated equilibrium states and (b) for a given saturated equilibrium state or a given pair of saturated equilibrium and initial states, which and how many gene networks, referred to as viable, share this saturated equilibrium state or the pair of saturated equilibrium and initial states. We also show that the viable networks sharing a given saturated equilibrium state must follow certain patterns. These capabilities of the analytical treatment make it possible to properly define and accurately determine robustness to noise and mutation for gene networks. Previous network research conclusions drawn from performing millions of simulations follow directly from the results of our analytical treatment. Furthermore, the analytical results provide criteria for the identification of model validity and suggest modified models of gene network dynamics. The yeast cell-cycle network is used as an illustration of the practical application of this analytical treatment.en_US
dc.format.extent1-27en_US
dc.language.isoen_USen_US
dc.relation.ispartofEURASIP Journal on Bioinformatics and Systems Biologyen_US
dc.rightsFinal published version. This is an open access article.en_US
dc.titleAnalysis of gene network robustness based on saturated fixed point attractorsen_US
dc.typeJournal Articleen_US
dc.identifier.doidoi:10.1186/1687-4153-2014-4-
dc.date.eissued2014-03-20en_US
dc.identifier.eissn1687-4153-
pu.type.symplectichttp://www.symplectic.co.uk/publications/atom-terms/1.0/journal-articleen_US

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