title: Similarity of phylogenetic trees as indicator of protein-protein interaction.
abstract: Deciphering the network of protein interactions that underlines cellular operations has become one of the main tasks of proteomics and computational biology. Recently, a set of bioinformatics approaches has emerged for the prediction of possible interactions by combining sequence and genomic information. Even though the initial results are very promising, the current methods are still far from perfect. We propose here a new way of discovering possible protein-protein interactions based on the comparison of the evolutionary distances between the sequences of the associated protein families, an idea based on previous observations of correspondence between the phylogenetic trees of associated proteins in systems such as ligands and receptors. Here, we extend the approach to different test sets, including the statistical evaluation of their capacity to predict protein interactions. To demonstrate the possibilities of the system to perform large-scale predictions of interactions, we present the application to a collection of more than 67 000 pairs of E.coli proteins, of which 2742 are predicted to correspond to interacting proteins.
authors.affiliation: Protein Design Group, CNB-CSIC, Cantoblanco, E-28049 Madrid, Spain.
authors.forename: F
authors.initials: F
authors.lastname: Pazos
authors.forename: A
authors.initials: A
authors.lastname: Valencia
mesh_terms: D018834:Chaperonin 60 / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D019143:Evolution, Molecular; D019204:GTP-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016680:Genome, Bacterial; D005975:Glutamate-tRNA Ligase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012269:Ribosomal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D013223:Statistics as Topic
chemical_list: D018834:Chaperonin 60; D029968:Escherichia coli Proteins; D020543:Proteome; D012269:Ribosomal Proteins; C036004:ribosomal protein S15; D019204:GTP-Binding Proteins; D005975:Glutamate-tRNA Ligase