Literature DB >> 16906869

Topology of resultant networks shaped by evolutionary pressure.

Avi Ma'ayan1, Azi Lipshtat, Ravi Iyengar.   

Abstract

Understanding the topology of complex systems abstracted to networks is important for unraveling their functional capabilities. Many such networks follow the small-world and scale-free regimes. Several models of artificially growing networks lead to this observed network topology. Most previously proposed models for growing networks, such as rich-get-richer and duplication-divergence, produce realistic network topologies but do not consider the effects of exogenous forces such as optimization for adaptation in shaping network topology. It is likely that such forces have shaped complex systems throughout their evolution. To develop further insights into possible mechanisms that shape networks, a model that uses several previously proposed network growth algorithms was developed to grow networks that adapt under exogenous stress. A decision tree problem was used to generate a complex Boolean function. Growing networks were required to adapt to correctly decode this function using an evolutionary selection process. Under this growth regimen all growing network models are similarly adaptable. The newly added nodes tend to cluster into pathways emanating from few inputs, regardless of the growth algorithm. Distribution of redundant pathways from inputs to the output follow a power-law function with a scaling exponent (approximately 1.3). Similar distribution of redundant pathways was observed from inputs in a cell signaling network and an air traffic control network. A flat distribution of redundant pathways from inputs was observed in growing networks that do not attempt to adapt. This analysis provides initial insights into distribution of pathways in naturally evolving complex systems that have defined input-output relationships.

Entities:  

Mesh:

Year:  2006        PMID: 16906869      PMCID: PMC3032447          DOI: 10.1103/PhysRevE.73.061912

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  16 in total

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4.  A duplication growth model of gene expression networks.

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5.  Preferential attachment in the protein network evolution.

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Journal:  Phys Rev Lett       Date:  2003-09-26       Impact factor: 9.161

6.  Evolving protein interaction networks through gene duplication.

Authors:  Romualdo Pastor-Satorras; Eric Smith; Ricard V Solé
Journal:  J Theor Biol       Date:  2003-05-21       Impact factor: 2.691

7.  Spatial growth of real-world networks.

Authors:  Marcus Kaiser; Claus C Hilgetag
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2004-03-09

8.  Formation of regulatory patterns during signal propagation in a Mammalian cellular network.

Authors:  Avi Ma'ayan; Sherry L Jenkins; Susana Neves; Anthony Hasseldine; Elizabeth Grace; Benjamin Dubin-Thaler; Narat J Eungdamrong; Gehzi Weng; Prahlad T Ram; J Jeremy Rice; Aaron Kershenbaum; Gustavo A Stolovitzky; Robert D Blitzer; Ravi Iyengar
Journal:  Science       Date:  2005-08-12       Impact factor: 47.728

9.  Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae.

Authors:  H Ge; Z Liu; G M Church; M Vidal
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

10.  A protein interaction map of Drosophila melanogaster.

Authors:  L Giot; J S Bader; C Brouwer; A Chaudhuri; B Kuang; Y Li; Y L Hao; C E Ooi; B Godwin; E Vitols; G Vijayadamodar; P Pochart; H Machineni; M Welsh; Y Kong; B Zerhusen; R Malcolm; Z Varrone; A Collis; M Minto; S Burgess; L McDaniel; E Stimpson; F Spriggs; J Williams; K Neurath; N Ioime; M Agee; E Voss; K Furtak; R Renzulli; N Aanensen; S Carrolla; E Bickelhaupt; Y Lazovatsky; A DaSilva; J Zhong; C A Stanyon; R L Finley; K P White; M Braverman; T Jarvie; S Gold; M Leach; J Knight; R A Shimkets; M P McKenna; J Chant; J M Rothberg
Journal:  Science       Date:  2003-11-06       Impact factor: 47.728

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  4 in total

1.  Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks.

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Review 2.  Insights into the organization of biochemical regulatory networks using graph theory analyses.

Authors:  Avi Ma'ayan
Journal:  J Biol Chem       Date:  2008-10-20       Impact factor: 5.157

3.  Functions of bifans in context of multiple regulatory motifs in signaling networks.

Authors:  Azi Lipshtat; Sudarshan P Purushothaman; Ravi Iyengar; Avi Ma'ayan
Journal:  Biophys J       Date:  2008-01-04       Impact factor: 4.033

4.  Evolution of complex modular biological networks.

Authors:  Arend Hintze; Christoph Adami
Journal:  PLoS Comput Biol       Date:  2008-02       Impact factor: 4.475

  4 in total

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