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Publication

Title:Increased genome sampling reveals a dynamic relationship between gene duplicability and the structure of the primate protein–protein interaction network
Authors:Doherty A., Alvarez-Ponce D. and McInerney J.O., 2012
Abstract: Although gene duplications occur at a high rate, only a small fraction of these are retained. The position of a gene's encoded product in the protein–protein interaction network has recently emerged as a determining factor of gene duplicability. However, the direction of the relationship between network centrality and duplicability is not universal: in Escherichia coli, yeast, fly and worm, duplicated genes more often act at the periphery of the network, whereas in humans such genes tend to occupy the most central positions. Here, we have inferred duplication events that took place in the different branches of the primate phylogeny. In agreement with previous observations, we found that duplications generally affected the most central network genes, which presumably is the process that has most influenced the trend in humans. However, the opposite trend, i.e. duplication being more common in genes whose encoded products are peripheral in the network, is observed for three recent branches, including, quite counter-intuitively, the external branch leading to humans. This indicates a shift in the relationship between centrality and duplicability during primate evolution. Furthermore, we found that genes encoding interacting proteins exhibit phylogenetic tree topologies that are more similar than expected for random pairs, and that genes duplicated in a given branch of the phylogeny tend to interact with those that duplicated in the same lineage. These results indicate that duplication of a gene increases the likelihood of duplication of its interacting partners. Our observations indicate that the structure of the primate protein–protein interaction network affects gene duplicability in previously unrecognized ways.
ICHEC Project:Analysing duplication patterns in interacting proteins in primates.
Publication:Molecular Biology & Evolution (2012) 29:3563-3573
URL: http://dx.doi.org/10.1093/molbev/mss165
Keywords: Gene duplicability; protein–protein interaction network; network evolution; primate evolution
Status: Published

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