Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Correspondence
  • Published:

Toward the complete interactome

Nature Biotechnology volume 24, pages 614–615 (2006)Cite this article

A Correspondence to this article was published on 01 June 2006

To the editor:

Incomplete protein-protein interaction networks obtained in high-throughput experiments are commonly used to characterize the topology of the complete interactome and are, in general, described as scale-free1. In the July issue, on the basis of simulations of network topologies, Marc Vidal and colleagues (Han et al., Nat. Biotechnol. 23, 839–884, 2005) argue that this apparent scale-free topology of experimental yeast two-hybrid interaction networks may be a consequence of the sampling process involved in the experimental set-up. By considering other network characteristics, in particular the average clustering coefficient2, it can be demonstrated that this conclusion is far too pessimistic.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Effect of sampling on the average clustering coefficient (CC) of networks.

References

  1. Jeong, H., Mason, S.P., Barabási, A.L. & Oltvai, Z.N. Nature 411, 41–42 (2001).

    Article  CAS  Google Scholar 

  2. Watts, D.J. & Strogatz, S.H. Nature 393, 440–442 (1998).

    Article  CAS  Google Scholar 

  3. Erdös, P. & Rényi, A. Publ. Math. Debrecen 6, 290–297 (1959).

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. LFE Bioinformatik, Institut für Informatik, Ludwig-Maximilians-Universität München, Amalienstraße 17, München, 80333, Germany

    Caroline C. Friedel & Ralf Zimmer

Authors
  1. Caroline C. Friedel
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ralf Zimmer
    View author publications

    You can also search for this author in PubMed Google Scholar

Supplementary information

Supplementary Fig. 1

Degree distributions for the theoretical network models. (PDF 127 kb)

Supplementary Fig. 2

Effect of sampling on the clustering coefficient for equal rates of bait and edge coverage. (PDF 41 kb)

Supplementary Fig. 3

Effect of sampling for all combinations of bait and edge coverage. (PDF 108 kb)

Supplementary Table 1

Characteristics of protein interaction maps. (PDF 22 kb)

Supplementary Table 2

Average clustering coefficient of simulated networks. (PDF 21 kb)

Supplementary Methods (PDF 60 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Friedel, C., Zimmer, R. Toward the complete interactome. Nat Biotechnol 24, 614–615 (2006). https://doi.org/10.1038/nbt0606-614

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt0606-614

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing