A constructive approach to gene expression dynamics

DOI10.1016/J.PHYSLETA.2004.07.045MaRDI QIDQ2425759zbMATH OpenOpenAlexFDO

Authors T. Ochiai, J. C. Nacher, Tatsuya Akutsu

Publication date 7 May 2008

Published in Physics Letters. A (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/q-bio/0406052

zbMATH Keywords

Markov propertyscale-free

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Genetics and epigenetics (92D10) Markov processes (60J99)

Abstract: The advent of new experimental genomic technologies and the massive increase of DNA sequence information is helping researchers better understand how our genes work. Recently, experiments on mRNA abundance (gene expression) have revealed that gene expression shows a stationary organization described by a power-law distribution (scale-free organization) (i.e., gene expression $k$ decays as $k^{-gamma}$), which is highly conserved in all the major five kingdoms of life, from Bacteria to Human. An underlying gene expression dynamics "rich-travel-more" was suggested to recover that evolutional conservation of transcriptional organization. Here we propose a constructive approach to gene expression dynamics with larger scope. Our gene expression construction restores the stationary state, predicts the power-law exponent for different organisms with natural explanation for small correction at high and low expression levels, describes the intermediate state dynamics (time finite) and elucidates the gene expression stability. This approach requires only one assumption: Markov property.

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Cites work

• scientific article; zbMATH DE number 3388297 (Why is no real title available?)
• Elementary Stochastic Calculus, with Finance in View
• Stochastic processes in physics and chemistry.

Cited in

(4)

• A stochastic approach to multi-gene expression dynamics
• ON THE RELATION BETWEEN FLUCTUATION AND SCALING-LAW IN GENE EXPRESSION TIME SERIES FROM YEAST TO HUMAN
• Power-law distribution of gene expression fluctuations
• Stochastic analysis of autoregulatory gene expression dynamics

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