Interactome Data
Over the past 10-15 years, we have developed a high-throughput pipeline to map high-quality binary protein-protein interactions at proteome scale for H. sapiens and a number of model organisms. All of our published and much of our pre-publication data is available to query or download via this link.
Human interactome
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Human 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 report ~14,000 new direct, binary interactions (Rolland et al Cell 2014), bringing the total number of unique binary interactions to ~17,000. Mapping of the reference human interactome has begun, with early release of human ORF collection for binary interaction screening and binary protein-protein interactions from a small test search space used to develop, optimize, and benchmark improvements to the mapping pipeline, as well as the release of preliminary data.
Learn more about the ongoing human interactome mapping project |
Yeast interactome
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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 (Ito et al PNAS 2001) and Uetz-screen (Uetz et al Nature 2000) datasets to produce Y2H-union, which contains 2,930 binary interactions among 2,018 proteins, ~20% of the whole yeast binary interactome.
Learn more about the ongoing yeast interactome mapping project |
FlyBi : D. megalonaster interactome
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The Drosophila melanogaster genome is one of the best-annotated multi-cellular eukaryotic genomes and yet our knowledge of protein-protein interactions (PPIs), protein complexes and networks in D. melanogaster proteomics is still limited. Drosophila is an important model for disease-focused and basic biological studies, and can be used for the study of conserved gene functions related to cancers, neurodegenerative diseases, diabetes. D. melanogaster also serves as a model for the study of insect pests and disease vectors such as mosquitos.
Together with the Berkeley Drosophila Genome Project (BDGP ) and the Drosophila RNAi Screening Center (DRSC ) we propose a state-of-the-art, high-throughput, quality-controlled binary protein interaction analysis with ~10,000 D. melanogaster open reading frames (ORFs), representing about two thirds of the proteome, to generate a high-confidence binary protein-protein interaction network. Using our established binary interaction mapping pipeline, we are screening 10,000 x 10,000 ORFs pairs for interactions with one another, i.e. testing ~100 million pairs. Primary screening and pairwise verification assays are performed using the yeast two-hybrid platform, followed by validation of the dataset using orthogonal orthogonal binary interaction assays, such as MAPPIT and GPCA. For more information about the FlyBi project, including information regarding distribution of FlyBi clones by repositories, please see http://flybi.hms.harvard.edu/ |
Virus-host interactome
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Viruses intrinsically depend on their host cell during the course of infection and can elicit pathological phenotypes similar to those arising from mutations (Gulbahce et al PLoS Comput Biol 2012). We applied a systematic integrated pipeline to investigate at genome-scale perturbations of host interactome networks induced by individual gene products encoded by members of four functionally related, yet biologically distinct, families of DNA tumor viruses: polymaviruses, papillomaviruses, adenoviruses, and Epstein-Barr virus (Rozenblatt-Rosen et al Nature 2012). By yeast two-hybrid we screened 123 viral ORFs against ~13,000 human ORFs, obtaining 454 validated binary interactions between 53 viral proteins and 307 human target proteins. By tandem affinity purification followed by mass spectrometry (TAP-MS), we reproducibly mapped 3,787 viral-host co-complex associations involving 54 viral proteins and the products of 1,079 unambiguously identified host genes.
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