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To combat false positive discoveries, a number of different methods have been recently developed that associate confidence scores with protein interactions. Here, we perform a rigorous comparative analysis and performance assessment among these different methods.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We measure the extent to which each set of confidence scores correlates with similarity of the interacting proteins in terms of function, expression, pattern of sequence conservation, and homology to interacting proteins in other species. We also employ a new metric, the Signal-to-Noise Ratio of protein complexes embedded in each network, to assess the power of the different methods. Seven confidence assignment schemes, including those of Bader <jats:italic>et al<\/jats:italic>., Deane <jats:italic>et al<\/jats:italic>., Deng <jats:italic>et al<\/jats:italic>., Sharan <jats:italic>et al<\/jats:italic>., and Qi <jats:italic>et al<\/jats:italic>., are compared in this work.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Although the performance of each assignment scheme varies depending on the particular metric used for assessment, we observe that Deng <jats:italic>et al<\/jats:italic>. yields the best performance overall (in three out of four viable measures). Importantly, we also find that utilizing any of the probability assignment schemes is always more beneficial than assuming all observed interactions to be true or equally likely.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-7-360","type":"journal-article","created":{"date-parts":[[2006,7,26]],"date-time":"2006-07-26T18:18:19Z","timestamp":1153937899000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":90,"title":["A direct comparison of protein interaction confidence assignment schemes"],"prefix":"10.1186","volume":"7","author":[{"given":"Silpa","family":"Suthram","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tomer","family":"Shlomi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eytan","family":"Ruppin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roded","family":"Sharan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Trey","family":"Ideker","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2006,7,26]]},"reference":[{"key":"1099_CR1","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1038\/340245a0","volume":"340","author":"S Fields","year":"1989","unstructured":"Fields S, Song O: A novel genetic system to detect protein-protein interactions. 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