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| Pedro Beltrao; Luis Serrano. |
| Progress in uncovering the protein interaction networks of several species has led to questions of what underlying principles might govern their organization. Few studies have tried to determine the impact of protein interaction network evolution on the observed physiological differences between species. Using comparative genomics and structural information, we show here that eukaryotic species have rewired their interactomes at a fast rate of approximately 10?5 interactions changed per protein pair, per million years of divergence. For Homo sapiens this corresponds to 103 interactions changed per million years. Additionally we find that the specificity of binding strongly determines the interaction turnover and that different biological processes show... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Evolutionary Biology. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/26/version/1 |
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| Pedro Beltrao. |
| It has been previously shown [1] that _S. cerevisiae_ proteins preferentially interact with proteins of the same estimated likely time of origin. To study this observation further, the protein interaction networks of _S. cerevisiae_ and _H. sapiens_ were analyzed taking into account an estimate for the age of the proteins in these species. These estimates were obtained by studying the presence and absence of putative orthologs in other eukaryotic species. In this work preliminary results are described that point to a dependence of the likelihood of protein interaction on the proteins’ age. The probability of two proteins interactions was found to be linearly dependent on the time the proteins have co-existed in the species. |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Evolutionary Biology. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/22/version/1 |
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| Pedro Beltrao; Luis Serrano. |
| Protein interaction networks are an important part of the post-genomic effort to integrate a part-list view of the cell into system-level understanding. Using a set of 11 yeast genomes we show that combining comparative genomics and secondary structure information greatly increases consensus-based prediction of SH3 targets. Benchmarking of our method against positive and negative standards gave 83% accuracy with 26% coverage. The concept of an optimal divergence time for effective comparative genomics studies was analyzed, demonstrating that genomes of species that diverged very recently from _Saccharomyces cerevisiae_ (_S. mikatae_, _S. bayanus_, and _S. paradoxus_), or a long time ago (_Neurospora crassa_ and _Schizosaccharomyces pombe_), contain less... |
| Tipo: Presentation |
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/16/version/1 |
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