WI-PHI: A Weighted Yeast Interactome Enriched for Direct Physical Interactions

Proteomics. 2007 Mar;7(6):932-43. doi: 10.1002/pmic.200600448.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anaphase-Promoting Complex-Cyclosome
  • Databases, Protein
  • Fungal Proteins / metabolism*
  • Protein Interaction Mapping
  • Proteome / analysis*
  • Reproducibility of Results
  • Ubiquitin-Protein Ligase Complexes / metabolism


  • Fungal Proteins
  • Proteome
  • Ubiquitin-Protein Ligase Complexes
  • Anaphase-Promoting Complex-Cyclosome