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On the number of protein-protein interactions in the yeast proteome - PubMed

  • ️Wed Jan 01 2003

Comparative Study

. 2003 Jul 15;31(14):4157-61.

doi: 10.1093/nar/gkg466.

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Comparative Study

On the number of protein-protein interactions in the yeast proteome

Andrei Grigoriev. Nucleic Acids Res. 2003.

Abstract

Using two different approaches, we estimated that on average there are about five interacting partners per protein in the proteome of the yeast Saccharomyces cerevisiae. In the first approach, we used a novel method to model sampling overlap by a Bernoulli process, compared the results of two independent yeast two-hybrid interaction screens and tested the robustness of the estimate. The most stable estimate of five interactors per protein was obtained when the three most highly connected nodes in the protein interaction network were removed from the analysis (eight interactors per protein if those nodes were kept). In the second approach, we analysed a published high-confidence subset of putative interaction data obtained from multiple sources, including large-scale two-hybrid screens, complex purifications, synthetic lethals, correlated gene expression, computational predictions and previous annotations. Strikingly, the estimate was again five interactors per protein. These estimates suggest a range of approximately 16,000-26,000 different interaction pairs in the yeast, excluding homotypic interactions. We also discuss the approaches to estimating the rate of homotypic interactions.

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Figures

Figure 1
Figure 1

Overlap of the protein–protein interactions for YGR119C. Green and red rectangles correspond to interacting partners from set I and set U, respectively. Partners common between sets I and U are shown as blue rectangles. In this example, nA = 5, nB = 4, nAB = 2, so the expected total number of partners of YGR119C is N = 10, though only seven are currently detected.

Figure 2
Figure 2

Overlap of the protein–protein interaction subnetworks. Subnetworks displayed are around the proteins encoded by YNL189W, YML064C and YLR423C (shown as white rectangles), the most highly connected nodes common for the datasets U and I (the u- and i- prefixes corresponds to sets U and I, respectively). The comparative display represents a screen shot of PINS (Protein Interaction Navigation System; Grigoriev, unpublished) software. Interaction partners are shown only for these three proteins. Color coding is as in Figure 1, while pink rectangles designate proteins linked to more than one of the above nodes.

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