Interactome Projects at CCSB

H uman interactome mapping is the flagship project of CCSB. A first map of the human binary interactome (Rual et al Nature 2005) was obtained by yeast two-hybrid (Y2H) screening for direct, binary interactions within a "Space-I" matrix of ~8,000 x 8,000 ORFs contained in Human ORFeome v1.1 (Rual et al Genome Res 2004). We have developed an empirical framework that quantitatively measures the parameters of screening completeness, assay sensitivity, sampling sensitivity, and precision, and used this framework to estimate the size of the human binary interactome as ~130,000 ± 32,000 binary interactions (Venkatesan et al Nat Methods 2009). Using a novel next-generation sequencing strategy to identify interaction pairs (Yu et al Nat Methods 2011), we have carried out a Y2H screen for interactions within a “Space-II” matrix of ~13,000 x 13,000 ORFs contained in Human ORFeome v5.1. We now provide prepublication to the community ~14,000 new direct, binary interactions (HI-2012 Prepublication), bringing the total number of unique binary interactions to ~17,000 and the completion of the Reference Human Interactome map to ~20%. more

Plants have unique features that evolved in response to environmental and ecological challenges. Accounts of the complex cellular networks that underlie plant-specific functions are missing. We reported a proteome-wide binary protein-protein interaction map from a search space size of ~8,000 x 8,000 ORFs for the interactome network of the plant Arabidopsis thaliana. This interactome map contains ~6,200 highly reliable interactions between ~2,700 proteins (Arabidopsis Interactome Mapping Consortium, Science 2011), representing ~2% of the full Arabidopsis biophysical binary interactome. more

Worm Interactome version 8 contains 3,864 binary protein-protein interactions for C. elegans assembled from the WI-2007 high-throughput yeast two-hybrid screen (1,816 new interactions reported in Simonis et al Nat Methods 2009); the WI-2004 high-throughput yeast two-hybrid screen (1,735 interactions reported in Li et al Science 2004); and a compendium of data from medium-throughput yeast two-hybrid screens (554 interactions). more

Yeast Interactome version 1 (CCSB-YI1) contains high-quality yeast two-hybrid protein-protein interactions for S. cerevisiae. It includes 1,809 interactions among 1,278 proteins, comprising ~10% of the complete yeast binary interactome estimated at ~18,000 ± 4,500 interactions (Yu et al Science 2008). To obtain a more comprehensive binary yeast interactome CCSB-YI1 was combined with Ito-core and Uetz-screen datasets to produce Y2H-union, which contains 2,930 binary interactions among 2,018 proteins, ~20% of the whole yeast binary interactome. more

Fragmentome: Many protein-protein interactions are mediated through independently folding modular domains. Proteome-wide efforts to model interactome networks have necessarily neglected the modular organization of proteins. We developed an experimental “fragmentome” strategy to efficiently identify interaction domains (Boxem et al Cell 2008). We used this strategy to generate a domain-based interactome network for proteins involved in C. elegans early embryonic cell divisions.