Toward a Comprehensive Atlas of the Physical Interactome of Saccharomyces cerevisiae*S

By Sean R. Collins, Patrick Kemmeren, Xuefang Zhao, Jack Greenblatt, Forrest A. Spencer, Frank C. P. Holstege, Jonathan S. Weissman, Nevan J. Krogan. Molecular & Cellular Proteomics, 2007

817 citations recorded by the source corpus.

Defining protein complexes is critical to virtually all aspects of cell biology. Two recent affinity purification/mass spectrometry studies in Saccharomyces cerevisiae have vastly increased the available protein interaction data. The practical utility of such high throughput interaction sets, however, is substantially decreased by the presence of false positives. Here we created a novel probabilistic metric that takes advantage of the high density of these data, including both the presence and absence of individual associations, to provide a measure of the relative confidence of each potential protein-protein interaction. This analysis largely overcomes the noise inherent in high throughput immunoprecipitation experiments. For example, of the 12,122 binary interactions in the general repository of interaction data (BioGRID) derived from these two studies, we marked 7504 as being of substantially lower confidence. Additionally, applying our metric and a stringent cutoff we identified a set of 9074 interactions (including 4456 that were not among the 12,122 interactions) with accuracy comparable to that of conventional small scale methodologies. Finally we organized proteins into coherent multisubunit complexes using hierarchical clustering. This work thus provides a highly accurate physical interaction map of yeast in a format that is readily accessible to the biological community.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1022261a01949036f7a9c6dc1b1eae60ca36feb8

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In Molecular Biology

1. Jure Leskovec
2. Jaewon Yang
3. Haiyuan Yu
4. Nevan J. Krogan
5. Natasa Przulj
6. Xiaoli Li
7. Min Wu
8. Chee Keong Kwoh

Citations in the corpus

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• Detecting overlapping protein complexes in protein-protein interaction networks (2012, methodology): “RNSC Collins [7] Krogan [6] Gavin [5] BioGRID [8] core extended Shuffling diversification length 5 9 9 9 9 Diversification frequency 50 20 20 20 20 Number of experiments 3 3 3 3 3 Naive stopping tolerance 10 10 20 20 20 Scaled stopping tolerance 5 5 1 5 5 Tabu length 100 10 50 100 10 Tabu tolerance ”
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