title: Computational verification of protein-protein interactions by orthologous co-expression.
abstract: BACKGROUND
  High-throughput methods identify an overwhelming number of protein-protein interactions. However, the limited accuracy of these methods results in the false identification of many spurious interactions. Accordingly, the resulting interactions are regarded as hypothetical and computational methods are needed to increase their confidence. Several methods have recently been suggested for this purpose including co-expression as a confidence measure for interacting proteins, but their performance is still quite poor.
  
  
  RESULTS
  We introduce a novel computational method for verification of protein-protein interactions based on the co-expression of orthologs of interacting partners. The performance of our method is analysed using known S. cerevisiae interactions, and is shown to overcome limitations of previous methods. We present specific examples of known and putative interactions that are detected by our method and not by previous methods, and suggest that they represent transient interactions that might have been conserved and stabilized in other species.
  
  
  CONCLUSIONS
  Co-expression of orthologous protein-pairs can be used to increase the confidence of hypothetical protein-protein interactions in S. cerevisiae as well as in other species. This approach may be especially useful for species with no available expression profiles and for transient interactions.
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. itay.tirosh@weizmann.ac.il <itay.tirosh@weizmann.ac.il>
authors.forename: Itay
authors.initials: I
authors.lastname: Tirosh
authors.forename: Naama
authors.initials: N
authors.lastname: Barkai
mesh_terms: D000818:Animals; D001665:Binding Sites; D003001:Cloning, Molecular; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D030541:Databases, Genetic; D030562:Databases, Protein; D005656:Fungal Proteins / Q000737:chemistry; D015870:Gene Expression; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D008968:Molecular Conformation; D011485:Protein Binding; D017510:Protein Folding; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry; D040901:Proteomics; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D016415:Sequence Alignment; D012984:Software
chemical_list: D005656:Fungal Proteins; D011506:Proteins
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