Kohara Y et al. (1994) Worm Breeder's Gazette "The C. elegans cDNA Project: A Progress Report."

Sugimoto A, Motohashi T, Tabara H, Watanabe H, Kohara Y

[Worm Breeder's Gazette, 1994]

The C.elegans cDNA project: A progress report Yuji Kohara, Tomoko Motohashi, Akiko Sugimoto, Hisako Watanabe and Hiroaki Tabara Gene Library Lab, National Institute of Genetics, Mishima 411, Japan. e-mail: ykohara@lddbj.nig.ac.jp

Philippe Lamesch et al. (2005) International Worm Meeting "Worm Interacome project"

Philippe Lamesch, Alex Smolyar, Tomoko Hirozane-Kishikawa, Camille Bex, Tong Hao, Jennifer Rosenberg, Ning Li, Nono Ayiviguedehoussou, Jean-Francois Rual, Amelie Dricot

[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.

Nicolas Simonis et al. (2007) International Worm Meeting "Expanding the C. elegans interactome map."

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.

Kohara Y et al. (1995) Worm Breeder's Gazette "The C. elegans cDNA Project: A Progress Report."

Kohara Y, Motohashi T, Watanabe H, Sugimoto A, Tabara H

[Worm Breeder's Gazette, 1995]

The C.elegans cDNA project: A progress report Yuji Kohara, Tomoko Motohashi, Akiko Sugimoto, Hisako Watanabe and Hiroaki Tabara Gene Library Lab, National Institute of Genetics, Mishima 411, Japan e-mail: ykohara/*ddbj.nig.ac.jp Tag sequencing is now on the third set of cDNA dones. After analysis of the first set of cDNA clones (some 4,400 clones), each 10,000 clones were picked up randomly from 3 different cDNA libraries (an embryonic cDNA library and libraries of >2kb cDNA and unfractionated cDNA made from mixed stage population). The total 30,000 clones were gridded and probed with the cDNA clones belonging to the species which had been represented by more than 4 clones in the analysis of the first set. A set of some 4,800 cDNA clones (the second set) were selected out of the unhybridized clones (from rare or not analyzed cDNA species) and has been subjected to the tag sequencing. This analysis produced 3,667 clean 3'-tags which gave 1,532 more unique cDNA species (see Fig.). As the next step, the grids were further screened with the cDNA probes the groups containing more than 4 clones at the point. A set of some 4,000 cDNA clones (the third set) was selected out of the unhybridized clones and tag sequencing has been continued on this set. The current status of our progress is that we have identified 3,324 unique cDNA species out of 7,647 clones (clean 3'-tags). The unique cDNA species were assigned serial numbers from CELK00001 to CELK03324. These analyses have also detected many pairs of clones which appeared to be generated by alternative splicing. In some cases, two groups were turned out that they were derived from the same gene but had different 3'-end sequences due to alternative splicing or differential poly-A addition. We are going to make a list of such differential splicings. BLASTX search showed that 653 groups out of the 1,816 groups identified through the analysis of the second and the third sets gave significant similarities (blastx score > 100), which are listed below. (Note; "-" in the column of "Frame" means BLASTX search was made using only 3'-tag sequences so far.) Mapping and in situ analysis are in progress.