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Comparative assessment of large-scale data sets of protein–protein interactions

Abstract

Comprehensive protein–protein interaction maps promise to reveal many aspects of the complex regulatory network underlying cellular function. Recently, large-scale approaches have predicted many new protein interactions in yeast. To measure their accuracy and potential as well as to identify biases, strengths and weaknesses, we compare the methods with each other and with a reference set of previously reported protein interactions.

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Figure 1: Large-scale interaction data and the distribution of interactions according to functional categories.
Figure 2: Quantitative comparison of interaction data sets.
Figure 3: A bias in interaction coverage from mRNA abundance data.
Figure 4: Protein localization and interaction coverage.

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Acknowledgements

We thank members of the Bork group, N. Paton, A. Brass, S. Cohen, A.-C. Gavin and B. Kuster for critical discussions, and Cellzome AG for access to their interaction data before publication. C.v.M. and P.B. are supported by Bundesministerium fur Bildung und Forschung, Germany, and work in Manchester is supported by the Biotechnology and Biological Sciences Research Council through its IGF (Investigating Gene Function) initiative. S.F. is supported by the National Center for Research Resources of the National Institutes of Health, and is an investigator of the Howard Hughes Medical Institute. S.F. and P.B. are supported by the Human Frontier Science Program.

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P.B. has a financial interest in Cellzome.

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von Mering, C., Krause, R., Snel, B. et al. Comparative assessment of large-scale data sets of protein–protein interactions. Nature 417, 399–403 (2002). https://doi.org/10.1038/nature750

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