Table 1.

Data sources

No.Attribute abbreviationProperty of single proteinProteome coverage, %*Attribute of protein pairNo. of pairs with attribute Data source
1DDDomain signature65A domain–domain signature combination that appears in interacting protein pairs more often than expected at random454,714Our analysis (5) using InterPro database (51); learned from the data and assigned by 3-fold cross-validation
2FoldProtein fold26A combination of folds that appears in interacting protein pairs more often than expected at random177,895Our analysis using protein fold assignments of Hegyi et al. (52); learned from the data and assigned by 3-fold cross-validation
3FENA NA Gene fusion event486Our analysis following Marcotte et al. (11) and Enright et al. (12)
4PPPhylogenetic profile100Consistent phylogenetic profiles822,789Our analysis following Pellegrini et al. (13)
5GNNA NA Conservation of gene neighborhood5,755von Mering et al. data (19)
6LocCellular localization72Colocalization3,497,490YPD (53) and Huh et al. (37)
7ProcCellular process59Shared cellular process634,302YPD (53)
8ExpmRNA expression pattern100Coexpression94,370Based on clustering of Ihmels et al. (54)
9RegTranscriptional regulation43.3Coregulation270,272YPD (53) and Lee et al. (55)
  • *Fraction of proteins in S. cerevisiae that are annotated by this feature.

  • No. of pairs with attributes among all possible ≈1.8 × 107 pairs in S. cerevisiae. Pairs with missing data were treated as not showing the attribute.

  • NA, not applicable.