Abstract
The comparison of pairs of gene duplications generated by small-scale duplications with those created by large-scale duplications shows that they differ in quantifiable ways. It is suggested that this is directly due to biases on the paths to gene retention rather than association with different functional categories.
Highlights
Genes in populations are in constant flux, being gained through duplication and occasionally retained or, more frequently, lost from the genome
Whole-genome duplicates (WGDs) paralog pairs are functionally more similar than small-scale duplicates (SSDs) paralogs By using the protein interaction network as a proxy for protein function, it is possible to investigate the functional similarity of each member of a duplicate gene pair on a large scale
We have demonstrated that genes originating from singlegene and whole-genome duplication events differ in quantifiable ways; whole-genome and small-scale duplication derived proteins are enriched for different categories of molecular functions
Summary
Genes in populations are in constant flux, being gained through duplication and occasionally retained or, more frequently, lost from the genome. The collection of genes commonly referred to as 'duplicates' do not represent a homogeneous set This is because duplicate genes can be generated through one of two main mechanisms, namely smallscale or large-scale duplication events, with the most extreme large-scale event being duplication of the entire genome. Genes resulting from these processes are distinct subsets of gene duplicates. Genome Biology 2007, Volume 8, Issue 10, Article R209 Hakes et al R209.2 previous studies investigating the functional fate and evolution of these genes have always treated them as a single homogeneous population (for instance [5,6]). Subtle differences may have consequences relating to the probabilities of different types of genes being retained after duplication
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