Literature DB >> 18946549

Origins of stochasticity and burstiness in high-dimensional biochemical networks.

Simon Rosenfeld1.   

Abstract

Two major approaches are known in the field of stochastic dynamics of intracellular biochemical networks. The first one places the focus of attention on the fact that many biochemical constituents vitally important for the network functionality may be present only in small quantities within the cell, and therefore the regulatory process is essentially discrete and prone to relatively big fluctuations. The second approach treats the regulatory process as essentially continuous. Complex pseudostochastic behavior in such processes may occur due to multistability and oscillatory motions within limit cycles. In this paper we outline the third scenario of stochasticity in the regulatory process. This scenario is only conceivable in high-dimensional highly nonlinear systems. In particular, we show that burstiness, a well-known phenomenon in the biology of gene expression, is a natural consequence of high dimensionality coupled with high nonlinearity. In mathematical terms, burstiness is associated with heavy-tailed probability distributions of stochastic processes describing the dynamics of the system. We demonstrate how the "shot" noise originates from purely deterministic behavior of the underlying dynamical system. We conclude that the limiting stochastic process may be accurately approximated by the "heavy-tailed" generalized Pareto process which is a direct mathematical expression of burstiness.

Year:  2008        PMID: 18946549      PMCID: PMC3171425          DOI: 10.1155/2009/362309

Source DB:  PubMed          Journal:  EURASIP J Bioinform Syst Biol        ISSN: 1687-4145


  37 in total

1.  Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations.

Authors:  T B Kepler; T C Elston
Journal:  Biophys J       Date:  2001-12       Impact factor: 4.033

Review 2.  Metabolomics--the link between genotypes and phenotypes.

Authors:  Oliver Fiehn
Journal:  Plant Mol Biol       Date:  2002-01       Impact factor: 4.076

Review 3.  Network biology: understanding the cell's functional organization.

Authors:  Albert-László Barabási; Zoltán N Oltvai
Journal:  Nat Rev Genet       Date:  2004-02       Impact factor: 53.242

Review 4.  Modelling gene networks at different organisational levels.

Authors:  Thomas Schlitt; Alvis Brazma
Journal:  FEBS Lett       Date:  2005-03-21       Impact factor: 4.124

5.  Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm.

Authors:  Shuhei Kimura; Kaori Ide; Aiko Kashihara; Makoto Kano; Mariko Hatakeyama; Ryoji Masui; Noriko Nakagawa; Shigeyuki Yokoyama; Seiki Kuramitsu; Akihiko Konagaya
Journal:  Bioinformatics       Date:  2004-10-28       Impact factor: 6.937

6.  Functional cooperativity between transcription factors UBF1 and SL1 mediates human ribosomal RNA synthesis.

Authors:  S P Bell; R M Learned; H M Jantzen; R Tjian
Journal:  Science       Date:  1988-09-02       Impact factor: 47.728

7.  Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions.

Authors:  M A Savageau
Journal:  J Theor Biol       Date:  1969-12       Impact factor: 2.691

8.  Biochemical systems analysis. 3. Dynamic solutions using a power-law approximation.

Authors:  M A Savageau
Journal:  J Theor Biol       Date:  1970-02       Impact factor: 2.691

Review 9.  Glycomics: an integrated systems approach to structure-function relationships of glycans.

Authors:  Rahul Raman; S Raguram; Ganesh Venkataraman; James C Paulson; Ram Sasisekharan
Journal:  Nat Methods       Date:  2005-11       Impact factor: 28.547

10.  RNA dynamics in live Escherichia coli cells.

Authors:  Ido Golding; Edward C Cox
Journal:  Proc Natl Acad Sci U S A       Date:  2004-07-26       Impact factor: 11.205

View more
  9 in total

Review 1.  Mathematical descriptions of biochemical networks: stability, stochasticity, evolution.

Authors:  Simon Rosenfeld
Journal:  Prog Biophys Mol Biol       Date:  2011-03-22       Impact factor: 3.667

2.  Do DNA microarrays tell the story of gene expression?

Authors:  Simon Rosenfeld
Journal:  Gene Regul Syst Bio       Date:  2010-06-29

3.  Critical self-organized self-sustained oscillations in large regulatory networks: towards understanding the gene expression initiation.

Authors:  Simon Rosenfeld
Journal:  Gene Regul Syst Bio       Date:  2011-03-22

4.  Biomolecular self-defense and futility of high-specificity therapeutic targeting.

Authors:  Simon Rosenfeld
Journal:  Gene Regul Syst Bio       Date:  2011-11-21

5.  Characteristics of transcriptional activity in nonlinear dynamics of genetic regulatory networks.

Authors:  Simon Rosenfeld
Journal:  Gene Regul Syst Bio       Date:  2009-10-19

6.  Systems biology and cancer prevention: all options on the table.

Authors:  Simon Rosenfeld; Izet Kapetanovic
Journal:  Gene Regul Syst Bio       Date:  2008-10-10

7.  Patterns of stochastic behavior in dynamically unstable high-dimensional biochemical networks.

Authors:  Simon Rosenfeld
Journal:  Gene Regul Syst Bio       Date:  2009-01-29

8.  Global consensus theorem and self-organized criticality: unifying principles for understanding self-organization, swarm intelligence and mechanisms of carcinogenesis.

Authors:  Simon Rosenfeld
Journal:  Gene Regul Syst Bio       Date:  2013-02-20

9.  Are the somatic mutation and tissue organization field theories of carcinogenesis incompatible?

Authors:  Simon Rosenfeld
Journal:  Cancer Inform       Date:  2013-12-01
  9 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.