Table I

Protein-protein interaction datasets

DIP-YEAST is the entire S. cerevisiae protein-protein interaction network extracted from the DIP database on November 19, 2001. INT contains all the interactions determined by at least one small scale experiment, whereas sets EC2 and EC3 contain interactions determined by at least two or three independent experiments, respectively. GY2H contains all the interactions reported in genome-wide protein-protein interaction screens, and GY2H′ is a subset of GY2H that excludes interactions occurring only in the ITO1 set. The ITO1, ITO2, … ITO8 are subsets of GY2H that contain all the interactions reported by Ito et al. (7, 16) as identified by at least 1, 2, … 8 ISTs. RND1–3 sets were generated by randomly selecting 100,000 protein-protein pairs that are not present in DIP. PVM is the subset of DIP-YEAST scored by the PVM method. CORE is the amalgamation of the INT, E2, and PVM subsets. DIP subsets. See “Experimental Procedures” for further details. SS, small scale experiments; HT, high throughput screens.

DatasetSSHTNumber of interactions
AllExpression data availableaPVM subsetbInteractions with paralogs
DIP-YEAST8063722514286083
INT224618069131857
EC21179976448910
EC3377322158300
GY2H611454946484474
GY2H′324428825272436
PVM1428117214281428
CORE3003243514282480
RND110000087368106299980
RND210000087324106099975
RND310000087330106099983
ITO1433739353653083
ITO2145412892361033
ITO3795696173550
ITO4571493131388
ITO5494404112314
ITO646232490246
ITO737126875202
ITO830723368173
ITO927019860150
  • a Data reported by Brown and co-workers (23).

  • b Those interactions selected from each of the datasets by PVM as correct.