Biosystems. 2006 Sep;85(3):177-200. Epub 2006 May 2.

Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence.

Source

Department of Computer Science, Memorial University of Newfoundland, St John's, NL, Canada. kuo@cs.mun.ca

Abstract

Topological measures of large-scale complex networks are applied to a specific artificial regulatory network model created through a whole genome duplication and divergence mechanism. This class of networks share topological features with natural transcriptional regulatory networks. Specifically, these networks display scale-free and small-world topology and possess subgraph distributions similar to those of natural networks. Thus, the topologies inherent in natural networks may be in part due to their method of creation rather than being exclusively shaped by subsequent evolution under selection. The evolvability of the dynamics of these networks is also examined by evolving networks in simulation to obtain three simple types of output dynamics. The networks obtained from this process show a wide variety of topologies and numbers of genes indicating that it is relatively easy to evolve these classes of dynamics in this model.

PMID:: 16650928; [PubMed - indexed for MEDLINE]

MeSH Terms, Substances

MeSH Terms

Substances

Proteins

LinkOut - more resources

Full Text Sources

Other Literature Sources

COS Scholar Universe

Molecular Biology Databases

Saccharomyces Genome Database

Supplemental Content

Save items

Related citations in PubMed

Modeling protein network evolution under genome duplication and domain shuffling. [BMC Syst Biol. 2007]
Modeling protein network evolution under genome duplication and domain shuffling.
Evlampiev K, Isambert H. BMC Syst Biol. 2007 Nov 13; 1:49. Epub 2007 Nov 13.
Conservation and topology of protein interaction networks under duplication-divergence evolution. [Proc Natl Acad Sci U S A. 2008]
Conservation and topology of protein interaction networks under duplication-divergence evolution.
Evlampiev K, Isambert H. Proc Natl Acad Sci U S A. 2008 Jul 22; 105(29):9863-8. Epub 2008 Jul 16.
Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network. [PLoS Comput Biol. 2007]
Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
Ward JJ, Thornton JM. PLoS Comput Biol. 2007 Oct; 3(10):1993-2002. Epub 2007 Aug 27.
Review Modelling in molecular biology: describing transcription regulatory networks at different scales. [Philos Trans R Soc Lond B Biol...]
Review Modelling in molecular biology: describing transcription regulatory networks at different scales.
Schlitt T, Brazma A. Philos Trans R Soc Lond B Biol Sci. 2006 Mar 29; 361(1467):483-94.
Review General trends in the evolution of prokaryotic transcriptional regulatory networks. [Genome Dyn. 2007]
Review General trends in the evolution of prokaryotic transcriptional regulatory networks.
Madan Babu M, Balaji S, Aravind L. Genome Dyn. 2007; 3:66-80.

See reviews... See all...

Cited by 6 PubMed Central articles

On the architecture of cell regulation networks. [BMC Syst Biol. 2011]
On the architecture of cell regulation networks.
Lan Y, Mezić I. BMC Syst Biol. 2011 Mar 2; 5:37. Epub 2011 Mar 2.
From evidence to inference: probing the evolution of protein interaction networks. [HFSP J. 2009]
From evidence to inference: probing the evolution of protein interaction networks.
Ratmann O, Wiuf C, Pinney JW. HFSP J. 2009 Oct; 3(5):290-306. Epub 2009 Oct 19.
Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach. [Genome Biol. 2008]
Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach.
Freyre-González JA, Alonso-Pavón JA, Treviño-Quintanilla LG, Collado-Vides J. Genome Biol. 2008 Oct 27; 9(10):R154. Epub 2008 Oct 27.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Network topology and the evolution of dynamics in an artificial genetic regulato...
Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence.
Biosystems. 2006 Sep ;85(3):177-200. Epub 2006 May 2 .

PubMed
Common and distinct neural correlates of obsessive-compulsive and related disord...
Common and distinct neural correlates of obsessive-compulsive and related disorders.
Psychiatr Clin North Am. 2006 Jun ;29(2):391-410, viii.

PubMed
The health migration crisis: the role of four Organisation for Economic Cooperat...
The health migration crisis: the role of four Organisation for Economic Cooperation and Development countries.
Lancet. 2006 Apr 29 ;367(9520):1448-55.

PubMed
Rate, extent, and modifiers of spermatogenic recovery after hormonal male contra...
Rate, extent, and modifiers of spermatogenic recovery after hormonal male contraception: an integrated analysis.
Lancet. 2006 Apr 29 ;367(9520):1412-20.

PubMed
Analgesic activity of a non-peptide imidazolidinedione somatostatin agonist: in ...
Analgesic activity of a non-peptide imidazolidinedione somatostatin agonist: in vitro and in vivo studies in rat.
Pain. 2006 Sep ;124(1-2):34-49. Epub 2006 May 2 .

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: