title: Selection of organisms for the co-evolution-based study of protein interactions.
abstract: BACKGROUND
  The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the mirrortree and related methodologies, is being widely used. Although dependence between the performance of these methods and the set of organisms used to build the trees was suspected, so far nobody assessed it in an exhaustive way, and, in general, previous works used as many organisms as possible. In this work we asses the effect of using different sets of organism (chosen according with various phylogenetic criteria) on the performance of this methodology in detecting protein interactions of different nature.
  
  
  RESULTS
  We show that the performance of three mirrortree-related methodologies depends on the set of organisms used for building the trees, and it is not always directly related to the number of organisms in a simple way. Certain subsets of organisms seem to be more suitable for the predictions of certain types of interactions. This relationship between type of interaction and optimal set of organism for detecting them makes sense in the light of the phylogenetic distribution of the organisms and the nature of the interactions.
  
  
  CONCLUSIONS
  In order to obtain an optimal performance when predicting protein interactions, it is recommended to use different sets of organisms depending on the available computational resources and data, as well as the type of interactions of interest.
authors.affiliation: Computational Systems Biology Group, National Centre for Biotechnology (CNB-CSIC), Cantoblanco, 28049 Madrid, Spain.
authors.forename: Dorota
authors.initials: D
authors.lastname: Herman
authors.forename: David
authors.initials: D
authors.lastname: Ochoa
authors.forename: David
authors.initials: D
authors.lastname: Juan
authors.forename: Daniel
authors.initials: D
authors.lastname: Lopez
authors.forename: Alfonso
authors.initials: A
authors.lastname: Valencia
authors.forename: Florencio
authors.initials: F
authors.lastname: Pazos
mesh_terms: D000465:Algorithms; D001105:Archaea / Q000378:metabolism; D001419:Bacteria / Q000378:metabolism; D019143:Evolution, Molecular; D010802:Phylogeny; D054730:Protein Interaction Domains and Motifs; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D011506:Proteins