Literature DB >> 18239727

Cliques and duplication-divergence network growth.

I Ispolatov1, Pl Krapivsky, I Mazo, A Yuryev.   

Abstract

A population of complete subgraphs or cliques in a protein network model is studied. The network evolves via duplication and divergence supplemented with linking a certain fraction of target-replica vertex pairs. We derive a clique population distribution, which scales linearly with the size of the network and is in a perfect agreement with numerical simulations. Fixing both parameters of the model so that the number of links and abundance of triangles are equal to those observed in the fruitfly protein-binding network, we precisely predict the 4- and 5-clique abundance. In addition, we show that such features as fat-tail degree distribution, various rates of average degree growth and nonaveraging, revealed recently for a particular case of a completely asymmetric divergence, are present in a general case of arbitrary divergence.

Year:  2005        PMID: 18239727      PMCID: PMC2222917          DOI: 10.1088/1367-2630/7/1/000

Source DB:  PubMed          Journal:  New J Phys        ISSN: 1367-2630            Impact factor:   3.729


  15 in total

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3.  Network motifs: simple building blocks of complex networks.

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4.  Infinite-order percolation and giant fluctuations in a protein interaction network.

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5.  Asymmetric sequence divergence of duplicate genes.

Authors:  Gavin C Conant; Andreas Wagner
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Review 6.  Duplication and divergence: the evolution of new genes and old ideas.

Authors:  John S Taylor; Jeroen Raes
Journal:  Annu Rev Genet       Date:  2004       Impact factor: 16.830

7.  Inferring network mechanisms: the Drosophila melanogaster protein interaction network.

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Journal:  Proc Natl Acad Sci U S A       Date:  2005-02-22       Impact factor: 11.205

8.  The ATM-related cofactor Tra1 is a component of the purified SAGA complex.

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  10 in total

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2.  Conservation and topology of protein interaction networks under duplication-divergence evolution.

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3.  A probabilistic model of neutral and selective dynamics of protein network evolution.

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8.  Questioning the ubiquity of neofunctionalization.

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9.  Evolutionary analysis and interaction prediction for protein-protein interaction network in geometric space.

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10.  A novel evolutionary model for constructing gene coexpression networks with comprehensive features.

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Journal:  BMC Bioinformatics       Date:  2019-09-06       Impact factor: 3.169

  10 in total

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