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Open Access Research article

A direct comparison of protein interaction confidence assignment schemes

Silpa Suthram12, Tomer Shlomi3, Eytan Ruppin3, Roded Sharan3 and Trey Ideker12*

Author Affiliations

1 Department of Bioengineering, University of California, San Diego, CA 92093, USA

2 Program in Bioinformatics, University of California, San Diego, CA 92093, USA

3 School of Computer Science, Tel-Aviv University, Tel Aviv 69978, Israel

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BMC Bioinformatics 2006, 7:360  doi:10.1186/1471-2105-7-360

Published: 26 July 2006



Recent technological advances have enabled high-throughput measurements of protein-protein interactions in the cell, producing large protein interaction networks for various species at an ever-growing pace. However, common technologies like yeast two-hybrid may experience high rates of false positive detection. 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.


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 et al., Deane et al., Deng et al., Sharan et al., and Qi et al., are compared in this work.


Although the performance of each assignment scheme varies depending on the particular metric used for assessment, we observe that Deng et al. 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.