Gene essentiality and the topology of protein interaction networks.
The mechanistic bases for gene essentiality and for cell mutational resistance have long been disputed. The recent availability of large protein interaction databases has fuelled the analysis of protein interaction networks and several authors have proposed that gene dispensability could be strongly related to some topological parameters of these networks. However, many results were based on protein interaction data whose biases were not taken into account. In this article, we show that the essentiality of a gene in yeast is poorly related to the number of interactants (or degree) of the corresponding protein and that the physiological consequences of gene deletions are unrelated to several other properties of proteins in the interaction networks, such as the average degrees of their nearest neighbours, their clustering coefficients or their relative distances. We also found that yeast protein interaction networks lack degree correlation, i.e. a propensity for their vertices to associate according to their degrees. Gene essentiality and more generally cell resistance against mutations thus seem largely unrelated to many parameters of protein network topology.
Coulomb
Stéphane
S
Service de Physique Théorique, CEA/Saclay-Orme des Merisiers, 91191 Gif-sur-Yvette Cedex, France.
Bauer
Michel
M
Bernard
Denis
D
Marsolier-Kergoat
Marie-Claude
MC
D019295:Computational Biology; D017353:Gene Deletion; D020043:Genes, Essential / Q000235:genetics*; D009154:Mutation / Q000235:genetics*; D025941:Protein Interaction Mapping; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*
D029701:Saccharomyces cerevisiae Proteins