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  • Not all scale-free networks are born equal [Elektronski vir] : the role of the seed graph in PPI network evolution
    Hormozdiari, Fereydoun ...
    The interactions among proteins in an organism can be represented as a protein-protein interaction (PPI) network, where each protein is represented with a node, and each interaction is represented ... with an edge between two nodes. As PPI networks of several model organisms become available, their topological features attract considerable attention. It is believed that the available PPI networks are (1) ŽŽsmall-worldʼʼ networks, and (2) their degree distribution is in the form of a ŽŽpower law.ʼʼ In other words, (1) it is possible to reach from a protein to any other protein in only a small (approximately six) number of hops, and (2) although most proteins have only afew interactions (one or two), there are a few proteins with many more interactions (200 or more) and that act as ŽŽhubs.ʼʼ It has thus been temptingto develop simple mathematical network generators with topological features similar to those of the available PPI networks. One such model, the ŽŽduplication model,ʼʼ is based on Ohnoʼs model of genome growth. It starts with a small ŽŽseed networkʼʼ and grows by ŽŽduplicatingʼʼ one of the existingnodes at a time, with an identical set of interactions; a randomly selected subset of these interactions is then deleted, and a few new interactions are added at random. It has been mathematically proven that the duplication model provides a small-world network and also has a power-law degree distribution. What we show in this paper is that by choosing the ŽŽrightʼʼ seed network, many other topological features of the available PPI networks can be captured by the duplication model. The right seed network in this case turns out to include two sizable ŽŽcliquesʼʼ (subnetworks where all node pairs are connected) with many interactions in between. In this paper, wealso consider the preferential attachment model, which again grows by addingto a seed network one node at a time and connecting the new node to every other node with probability proportional to the existing degree of the second node. Because the preferential attachment model also provides a small-world network and has a power-law degree distribution, it has been considered equivalent to the duplication model. We show that the two models are vastly different in terms of other topological features we consider, and the preferential attachment model cannot capture some key features of the available PPI networks.
    Source: PLoS computational biology. - ISSN 1553-734X (Vol. 3, iss. 7, Jul. 2007, str. 1373-1384)
    Type of material - e-article ; adult, serious
    Publish date - 2007
    Language - english
    COBISS.SI-ID - 1024348993
    DOI

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