[
International Worm Meeting,
2005]
We generated a C. elegans interactome map that contains ~5,500 potential interactions, referred to as Worm Interactome version 5 (WI5) (Li et al. Science 2004). Together with another interactome map for Drosophila melanogaster, these datasets represent the first of their kind for metazoan organisms. Although already helpful, the protein interaction data in WI5 is far from complete and needs improvement. Here we describe the initiation of a new approach for the generation of a worm interactome version 6 (WI6). The first challenge of the WI6 project consisted in the generation of a worm ORFeome resource referred to as the worm ORFeome version 1. This collection of ~11,000 cloned ORFs represents a useful platform for the application of reverse proteomic approaches for worm. The WI6 project uses the worm ORFeome version 1 as a starting point, and is designed to cover three fundamental aspects of the interactome map: completeness, coverage, and quality. The second challenge was the development of an improved version of the yeast two-hybrid system. The goal of the WI6 project is to test all 11,000 cloned ORFs by yeast two-hybrid (Y2H) (1,21 x 108 pairwise combinations). We devised and validated a new protocol that combines both efficient HT settings and high level of saturation. The production phase of the project was recently initiated. We are able to test ~4 x 106 pairwise combinations per week. So far, we tested ~10% of the total matrix and found ~400 novel Y2H interactions. We expect to map an additional ~4,000 interactions by the end of the WI6 project. Successive interactome versions depend upon improvements in genome annotation and the progress of the ORFeome cloning project. Gradually our goal will be to expand the worm interactome map into more complete versions. Our ORFeome project has now evolved into a version 3.1 (see Abstract by Lamesch et al.), from which approximately 2,000 additional ORFs have been cloned. Ultimately, the aim is to generate a high quality interactome map that, together with other functional genomic and proteomic (or omic) information (Vidal Cell 2001), will serve as a backbone for the drawing of a global functional wiring diagram. The work in progress will be presented.
Michael Cusick, Julie Sahalie, David Hill, Mike Boxem, Jean-Francois Rual, Irma Lemmens, Anne-Ruxandra Carvunis, Chenwei Lin, Niels Klitgord, Amelie Dricot, David Szeto, Muhammed Yildirim, Nicolas Simonis, Fana Gebreab, Jan Tavernier, Marc Vidal, Alex Smolyar, Tong Hao, Tomoko Hirozane-Kishikawa, Pascal Braun
[
International Worm Meeting,
2007]
Systematic identification of protein-protein interactions is of immense value for cell and systems biology. Large-scale mapping of protein-protein interactions provides novel functional categorization of uncharacterized proteins and characterized proteins alike, and informs upon the emergent global properties of cellular networks. In pursuit of these aims we will present an expanded version of the C. elegans protein-protein interaction network, or interactome, map. Our last release, worm interactome 5 (WI5), focused on a subset of predicted worm proteins that have a clear ortholog in other multicellular organisms, and contained 1,039 high-confidence interactions representing ~3-5% of the predicted C. elegans interactome. Here we attempted to test all potential interactions in a matrix of ~11,000 x ~11,000 ORFs using an improved highly specific version of the high-throughput yeast two-hybrid (HT-Y2H) system, covering ~25% of the search space of the worm interactome. We identified 1,899 high-quality interactions, of which 1,643 are new. The technical quality of the interactions is being assessed by an orthogonal assay (MAPPIT), while the biological relevance is being estimated by comparing co-expression and Gene Ontology annotations of interacting pairs. The comparison of this new screen with the WI5 HT-Y2H experiment, which was performed with a very different strategy, allows estimations of the coverage and reproducibility of these two screens. Previous interactions from high-throughput, medium-throughput and literature curated datasets have been reprocessed according to new quality criteria and incorporated with the new HT-Y2H screen to generate a consolidated map (WI8) of 4,196 high quality binary interactions between 2,624 protein coding genes. Integration of WI8 with expression, genetic interaction, phenotypic and interolog data is being used to delineate functional modules, which will lead to new functional predictions for numerous genes.