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Bursting noise in gene expression dynamics: linking microscopic and mesoscopic models.

Lin YT, Galla T - J R Soc Interface (2016)

Bottom Line: The dynamics of short-lived mRNA results in bursts of protein production in gene regulatory networks.We investigate the propagation of bursting noise between different levels of mathematical modelling and demonstrate that conventional approaches based on diffusion approximations can fail to capture bursting noise.An alternative coarse-grained model, the so-called piecewise deterministic Markov process (PDMP), is seen to outperform the diffusion approximation in biologically relevant parameter regimes.

View Article: PubMed Central - PubMed

Affiliation: Theoretical Physics, School of Physics and Astronomy, The University of Manchester, Manchester M13 9PL, UK yenting.lin@manchester.ac.uk.

No MeSH data available.


MFST as a function of the initial protein numbers ( shown on a linear scale). (a) FM: full model; (b) GB model. (Online version in colour.)
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RSIF20150772F3: MFST as a function of the initial protein numbers ( shown on a linear scale). (a) FM: full model; (b) GB model. (Online version in colour.)

Mentions: Sweeping across the space of possible initial configuration, the MFST of the FM and of the GB model are measured in simulations and presented in figure 3. We show the MFST of the CB in the electronic supplementary material. As with the stationary distributions, the data in figure 3 indicate that the GB model approximates the switching times of the FM to a good accuracy. A more detailed quantitative comparison is again provided in the electronic supplementary material. We remark that the MFST of the CB model is almost twice as long as that of the GB and FM models, and the switching time in the NB model is longer than 1000 cell cycles (see the electronic supplementary material).Figure 3.


Bursting noise in gene expression dynamics: linking microscopic and mesoscopic models.

Lin YT, Galla T - J R Soc Interface (2016)

MFST as a function of the initial protein numbers ( shown on a linear scale). (a) FM: full model; (b) GB model. (Online version in colour.)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4759790&req=5

RSIF20150772F3: MFST as a function of the initial protein numbers ( shown on a linear scale). (a) FM: full model; (b) GB model. (Online version in colour.)
Mentions: Sweeping across the space of possible initial configuration, the MFST of the FM and of the GB model are measured in simulations and presented in figure 3. We show the MFST of the CB in the electronic supplementary material. As with the stationary distributions, the data in figure 3 indicate that the GB model approximates the switching times of the FM to a good accuracy. A more detailed quantitative comparison is again provided in the electronic supplementary material. We remark that the MFST of the CB model is almost twice as long as that of the GB and FM models, and the switching time in the NB model is longer than 1000 cell cycles (see the electronic supplementary material).Figure 3.

Bottom Line: The dynamics of short-lived mRNA results in bursts of protein production in gene regulatory networks.We investigate the propagation of bursting noise between different levels of mathematical modelling and demonstrate that conventional approaches based on diffusion approximations can fail to capture bursting noise.An alternative coarse-grained model, the so-called piecewise deterministic Markov process (PDMP), is seen to outperform the diffusion approximation in biologically relevant parameter regimes.

View Article: PubMed Central - PubMed

Affiliation: Theoretical Physics, School of Physics and Astronomy, The University of Manchester, Manchester M13 9PL, UK yenting.lin@manchester.ac.uk.

No MeSH data available.