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Related Experiment Videos

Stable evolutionary signal in a yeast protein interaction network.

Stefan Wuchty1, Albert-Laszlo Barabási, Michael T Ferdig

  • 1Northwestern Institute on Complexity, Chambers Hall, Northwestern University, Evanston, IL 60202, USA. s-wuchty@northwestern.edu

BMC Evolutionary Biology
|January 31, 2006
PubMed
Summary

Protein interaction networks offer cellular insights, but data noise is a challenge. This study shows that conserved protein interactions, indicated by high local clustering, are reliable evolutionary signals, useful for inferring network structures in non-model organisms.

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Area of Science:

  • Systems Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Protein interaction networks provide insights into cellular mechanisms.
  • False positives and negatives in protein-protein interaction data limit network utility.
  • Previous studies focused on individual protein conservation; this work examines interaction conservation.

Purpose of the Study:

  • To investigate the evolutionary persistence of 'link' based signals in protein interaction networks.
  • To assess the reliability of protein-protein interaction data using evolutionary conservation.
  • To demonstrate the utility of network topology for inferring structures in non-model organisms.

Main Methods:

  • Analysis of protein interaction network in Saccharomyces cerevisiae.

Related Experiment Videos

  • Evaluation of evolutionary conservation of interacting proteins.
  • Correlation analysis of local clustering, evolutionary conservation, and coexpression.
  • Comparative analysis using P. falciparum/Yeast orthologs.

    • Main Results:

    • Highly connected proteins show stable evolutionary conservation despite noisy interaction data.
    • Local clustering around protein interactions correlates with evolutionary conservation.
    • High local clustering is associated with elevated coexpression of interacting proteins.
    • Network topology can deduce local network structure in non-model organisms.

    Conclusions:

    • High local clustering signifies reliable protein interactions, linked to evolutionary conservation and coexpression.
    • Evolutionary units extend beyond single proteins to include their interactions.
    • Empirical interaction data, combined with orthologous clustering, can reliably infer network structures in non-model organisms.