Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

@article{citeulike:694902, abstract = {BACKGROUND:The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions. Sparse coverage in HTP datasets may, however, distort network properties and confound predictions. Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference.RESULTS:We describe here a comprehensive database of genetic and protein interactions, and associated experimental evidence, for the budding yeast Saccharomyces cerevisiae, as manually curated from over 31,793 abstracts and online publications. This literature-curated (LC) dataset contains 33,311 interactions, on the order of all extant HTP datasets combined. Surprisingly, HTP protein-interaction datasets currently achieve only around 14\% coverage of the interactions in the literature. The LC network nevertheless shares attributes with HTP networks, including scale-free connectivity and correlations between interactions, abundance, localization, and expression. We find that essential genes or proteins are enriched for interactions with other essential genes or proteins, suggesting that the global network may be functionally unified. This interconnectivity is supported by a substantial overlap of protein and genetic interactions in the LC dataset. We show that the LC dataset considerably improves the predictive power of network-analysis approaches. The full LC dataset is available at the BioGRID (http://www.thebiogrid.org) and SGD (http://www.yeastgenome.org/) databases.CONCLUSION:Comprehensive datasets of biological interactions derived from the primary literature provide critical benchmarks for HTP methods, augment functional prediction, and reveal system-level attributes of biological networks.}, author = {Reguly, Teresa and Breitkreutz, Ashton and Boucher, Lorrie and Breitkreutz, Bobby-Joe and Hon, Gary C. and Myers, Chad L. and Parsons, Ainslie and Friesen, Helena and Oughtred, Rose and Tong, Amy and Stark, Chris and Ho, Yuen and Botstein, David and Andrews, Brenda and Boone, Charles and Troyanskya, Olga G. and Ideker, Trey and Dolinski, Kara and Batada, Nizar N. and Tyers, Mike }, citeulike-article-id = {694902}, doi = {10.1186/jbiol36}, issn = {1475-4924}, journal = {Journal of Biology}, keywords = {annotation}, month = {June}, number = {4}, pages = {11+}, posted-at = {2007-11-16 13:05:34}, priority = {2}, title = {Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae}, url = {http://dx.doi.org/10.1186/jbiol36}, volume = {5}, year = {2006} }

TY - JOUR ID - citeulike:694902 L3 - citeulike-article-id:694902 TI - Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae JF - Journal of Biology VL - 5 IS - 4 SP - 11 SN - 1475-4924 N2 - BACKGROUND:The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions. Sparse coverage in HTP datasets may, however, distort network properties and confound predictions. Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference.RESULTS:We describe here a comprehensive database of genetic and protein interactions, and associated experimental evidence, for the budding yeast Saccharomyces cerevisiae, as manually curated from over 31,793 abstracts and online publications. This literature-curated (LC) dataset contains 33,311 interactions, on the order of all extant HTP datasets combined. Surprisingly, HTP protein-interaction datasets currently achieve only around 14% coverage of the interactions in the literature. The LC network nevertheless shares attributes with HTP networks, including scale-free connectivity and correlations between interactions, abundance, localization, and expression. We find that essential genes or proteins are enriched for interactions with other essential genes or proteins, suggesting that the global network may be functionally unified. This interconnectivity is supported by a substantial overlap of protein and genetic interactions in the LC dataset. We show that the LC dataset considerably improves the predictive power of network-analysis approaches. The full LC dataset is available at the BioGRID (http://www.thebiogrid.org) and SGD (http://www.yeastgenome.org/) databases.CONCLUSION:Comprehensive datasets of biological interactions derived from the primary literature provide critical benchmarks for HTP methods, augment functional prediction, and reveal system-level attributes of biological networks. KW - annotation AU - Reguly, Teresa AU - Breitkreutz, Ashton AU - Boucher, Lorrie AU - Breitkreutz, Bobby-Joe AU - Hon, Gary AU - Myers, Chad AU - Parsons, Ainslie AU - Friesen, Helena AU - Oughtred, Rose AU - Tong, Amy AU - Stark, Chris AU - Ho, Yuen AU - Botstein, David AU - Andrews, Brenda AU - Boone, Charles AU - Troyanskya, Olga AU - Ideker, Trey AU - Dolinski, Kara AU - Batada, Nizar AU - Tyers, Mike PY - 2006/06/08/ UR - http://dx.doi.org/10.1186/jbiol36 ER -