An information theoretic approach to constructing robust Boolean gene regulatory networks

IEEE/ACM Transactions on Computational Biology and Bioinformatics
Bane VasićAnantha Raman Krishnan

Abstract

We introduce a class of finite systems models of gene regulatory networks exhibiting behavior of the cell cycle. The model is an extension of a Boolean network model. The system spontaneously cycles through a finite set of internal states, tracking the increase of an external factor such as cell mass, and also exhibits checkpoints in which errors in gene expression levels due to cellular noise are automatically corrected. We present a 7-gene network based on Projective Geometry codes, which can correct, at every given time, one gene expression error. The topology of a network is highly symmetric and requires using only simple Boolean functions that can be synthesized using genes of various organisms. The attractor structure of the Boolean network contains a single cycle attractor. It is the smallest nontrivial network with such high robustness. The methodology allows construction of artificial cell cycle gene regulatory networks with the number of phases larger than in natural cell cycle.

References

Sep 7, 1987·Journal of Theoretical Biology·S Kauffman, S Levin
Apr 1, 1993·Origins of Life and Evolution of the Biosphere : the Journal of the International Society for the Study of the Origin of Life·L MerleA Szemzö
Feb 1, 1993·Current Opinion in Cell Biology·M Stewart
Sep 29, 1995·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·K Nasmyth
Mar 31, 1999·Trends in Genetics : TIG·H H McAdams, A Arkin
Jan 19, 2000·Molecular Biology of the Cell·K C ChenJ J Tyson
Jul 15, 2000·Neuron·P SmolenJ H Byrne
Sep 27, 2000·Proceedings of the National Academy of Sciences of the United States of America·L A AmaralH E Stanley
Apr 3, 2001·Nature Reviews. Genetics·J HastyJ J Collins
Apr 19, 2003·Proceedings of the National Academy of Sciences of the United States of America·Nicolas E BuchlerTerence Hwa
Oct 7, 2003·Annual Review of Biomedical Engineering·Mads KaernJ J Collins
Mar 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Fangting LiChao Tang
May 26, 2004·Proceedings of the National Academy of Sciences of the United States of America·Hideki KobayashiJames J Collins
Sep 3, 2004·Nature·Christopher T HarbisonRichard A Young
Dec 2, 2004·Proceedings of the National Academy of Sciences of the United States of America·S KauffmanCarl Troein
Sep 6, 2005·Metabolic Engineering·Beat P KramerMartin Fussenegger
Sep 10, 2005·Bioinformatics·Ranadip PalEdward R Dougherty
Apr 7, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Chen-Hsiang Yeang, Tommi Jaakkola
Dec 5, 2006·PLoS Computational Biology·Rutger HermsenPieter Rein ten Wolde
Feb 10, 2007·Genes & Development·David A DrubinPamela A Silver
Aug 19, 2007·Nature Reviews. Genetics·Andreas BeyerTrey Ideker
Oct 16, 2007·Journal of Theoretical Biology·Kai Willadsen, Janet Wiles
Feb 8, 2008·EURASIP Journal on Bioinformatics & Systems Biology·Nestor Walter TrepodeRonaldo Fumio Hashimoto
Feb 28, 2008·PloS One·Maria Davidich, Stefan Bornholdt
Nov 4, 2008·PloS One·Elena R Alvarez-BuyllaPablo Padilla-Longoria
Feb 3, 2009·Journal of Theoretical Biology·D J Irons
Mar 24, 2009·FEBS Letters·Wen-Bin Lee, Jiun-Yan Huang
May 30, 2009·Bioinformatics·Abhishek GargIoannis Xenarios
Sep 19, 2009·Molecular BioSystems·Adrien Fauré, Denis Thieffry
Jan 26, 2010·Journal of the Royal Society, Interface·Natalja Strelkowa, Mauricio Barahona
Feb 4, 2010·PloS One·Karan ManglaMark A Horowitz
Dec 4, 2010·Science·Sourav BandyopadhyayTrey Ideker

Related Concepts

Cell Cycle
Information Theory
Computational Molecular Biology
Gene Modules
Cell Cycle
Projections and Predictions
Gene Expression
Genes
Neural Networks (Anatomic)
Finite Element Analysis

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