The Yeast Reference Interactome
Literature Benchmark
5209
Mission
The Center for Cancer Systems Biology (CCSB) at Dana-Farber Cancer Institute is expanding on previous mapping efforts by constructing a proteome-wide map of binary yeast protein-protein interactions, testing ~99% of the SGD-annotated yeast protein-coding genes. All pairwise combinations of yeast protein-coding genes, for which we have a clone available, have been interrogated systematically to identify binary protein-protein interactions, leading to the generation of a fourth map of the yeast protein-protein interactome, referred as YI-II that has been integrated with previously published systematic maps.
Method
Pairwise combinations of yeast protein-coding genes were tested systematically using high throughput yeast two-hybrid (Y2H) screens to detect protein-protein interactions. All four systematic maps were generated using different assay versions of the canonical yeast two-hybrid system, described in table 1. For maps generated at CCSB (Yu et al and YI-II), the precision of the dataset was tested by validating some of the interactions in multiple orthogonal assays (Venkatesan et al). In total, 4,556 high-quality protein-protein interactions (PPIs) involving 2,552 proteins have been identified by the four maps.
Table 1: Summary of Y2H assay versions
Version |
Strains |
Vector details |
||
|
Plasmid |
Yeast origin of replication |
Reporters |
||
|
Uetz screen |
YULH, N106r |
pOBD2, pOAD |
CEN |
GAL1::URA3, GAL1::lacZ |
|
Ito core |
PJ69-2A, MaV204K |
pGBK-RC, pGAD-RD |
CEN |
GAL1::HIS3, GAL2::ADE2, SPAL10::URA3 |
|
YI-I |
Y8800, Y8930 |
pDEST-DB, pDEST-AD |
CEN |
GAL1::HIS3, GAL2::ADE2 |
|
YI-II |
Y8800, Y8930 |
pQZ212, pQZ213 |
2µ |
GAL1::HIS3, GAL2::ADE2 |
In addition to systematically identifying PPIs experimentally, the yeast interactome map also contains PPIs of comparable high quality from literature curation databases. This subset of literature-curated PPIs currently comprises 5,589 PPIs.