title: WI-PHI: a weighted yeast interactome enriched for direct physical interactions.
abstract: How is the yeast proteome wired? This important question, central in yeast systems biology, remains unanswered in spite of the abundance of protein interaction data from high-throughput experiments. Unfortunately, these large-scale studies show striking discrepancies in their results and coverage such that biologists scrutinizing the "interactome" are often confounded by a mix of established physical interactions, functional associations, and experimental artifacts. This stimulated early attempts to integrate the available information and produce a list of protein interactions ranked according to an estimated functional reliability. The recent publication of the results of two large protein interaction experiments and the completion of a comprehensive literature curation effort has more than doubled the available information on the wiring of the yeast proteome. This motivates a fresh approach to the compilation of a yeast interactome based purely on evidence of physical interaction. We present a procedure exploiting both heuristic and probabilistic strategies to draft the yeast interactome taking advantage of various heterogeneous data sources: application of tandem affinity purification coupled to MS (TAP-MS), large-scale yeast two-hybrid studies, and results of small-scale experiments stored in dedicated databases. The end result is WI-PHI, a weighted network encompassing a large majority of yeast proteins.
authors.affiliation: Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy.
authors.forename: Lars
authors.initials: L
authors.lastname: Kiemer
authors.forename: Stefano
authors.initials: S
authors.lastname: Costa
authors.forename: Marius
authors.initials: M
authors.lastname: Ueffing
authors.forename: Gianni
authors.initials: G
authors.lastname: Cesareni
mesh_terms: D064173:Anaphase-Promoting Complex-Cyclosome; D030562:Databases, Protein; D005656:Fungal Proteins / Q000378:metabolism*; D025941:Protein Interaction Mapping; D020543:Proteome / Q000032:analysis*; D015203:Reproducibility of Results; D043743:Ubiquitin-Protein Ligase Complexes / Q000378:metabolism
chemical_list: D005656:Fungal Proteins; D020543:Proteome; D043743:Ubiquitin-Protein Ligase Complexes; D064173:Anaphase-Promoting Complex-Cyclosome