Local modeling of global interactome networks

Denise Scholtens*, Marc Vidal, Robert Gentleman

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

18 Scopus citations


Motivation: Systems biology requires accurate models of protein complexes, including physical interactions that assemble and regulate these molecular machines. Yeast two-hybrid (Y2H) and affinity-purification/mass-spectrometry (AP-MS) technologies measure different protein-protein relationships, and issues of completeness, sensitivity and specificity fuel debate over which is best for high-throughput 'interactome' data collection. Static graphs currently used to model Y2H and AP-MS data neglect dynamic and spatial aspects of macromolecular complexes and pleiotropic protein function. Results: We apply the local modeling methodology proposed by Scholtens and Gentleman (2004) to two publicly available datasets and demonstrate its uses, interpretation and limitations. Specifically, we use this technology to address four major issues pertaining to protein-protein networks. (1) We motivate the need to move from static global interactome graphs to local protein complex models. (2) We formally show that accurate local interactome models require both Y2H and AP-MS data, even in idealized situations. (3) We briefly discuss experimental design issues and how bait selection affects interpretability of results. (4) We point to the implications of local modeling for systems biology including functional annotation, new complex prediction, pathway interactivity and coordination with gene-expression data.

Original languageEnglish (US)
Pages (from-to)3548-3557
Number of pages10
Issue number17
StatePublished - Sep 1 2005

ASJC Scopus subject areas

  • Computational Mathematics
  • Molecular Biology
  • Biochemistry
  • Statistics and Probability
  • Computer Science Applications
  • Computational Theory and Mathematics


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