| IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 1 Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach (2007) | |||||||||||||||||
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| The goal of contemporary proteome research is the elucidation of protein interactions in the cell. Based on cur-rently available protein-protein interaction and domain data of S. cerevisiae, we introduce a novel method, Maximum Specificity Set Cover (MSSC), to predict protein-protein interactions. Our approach features two stages: First, we select high quality protein interactions based on a clustering measure. Second, we use MSSC to assign probabilities to domain pairs. This approach allows us to predict previously unknown protein-protein interactions with a degree of sensitivity and specificity that clearly outscores other approaches. We achieve 86 % sensitivity and 62 % specificity using 80 % of the high quality interactions in the DIP database. We find that the predicted interaction network preserves the characteristics of the initial web of known protein interactions. We also observe high levels of co-expression among putative interactions. Index Terms F.2.2.b Computations on discrete structures, G.2.2.a Graph algorithms, H.2.8.a Bioinformatics (genome or protein) | |||||||||||||||||
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