Filtering and Interpreting Large-Scale Experimental Protein–Protein Interaction Data

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 781)

Abstract

Rarely acting in isolation, it is invariably the physical associations among proteins that define their biological activity, necessitating the study of the cellular meshwork of protein–protein interactions (PPI) before a full appreciation of gene function can be achieved. The past few years have seen a marked expansion in the both the sheer volume and number of organisms for which high-quality interaction data is available, with high-throughput interaction screening and detection techniques showing consistent improvement both in scale and sensitivity. Although techniques for large-scale PPI mapping are increasingly being applied to new organisms, including human, there is a corresponding need to rigorously evaluate, benchmark, and impartially filter the results. This chapter explores methods for PPI dataset evaluation, including a survey of previous techniques applied by landmark studies in the field and a discussion of promising new experimental approaches. We further outline practical suggestions and useful tools for interpreting newly generated PPI data. As the majority of large-scale experimental data has been generated for the budding yeast S. cerevisiae, most of the techniques and datasets described are from the perspective of this model unicellular eukaryote; however, extensions to other organisms including mammals are mentioned where possible.

Key words

Protein–protein interaction Network Affinity purification Mass spectrometry Yeast 2-hybrid Large-scale assay Systems biology 
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Notes

Acknowledgments

AE and ZZ acknowledge a Team Grant from the Canadian Institute of Health Research (CIHR MOP#82940).

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Cardiovascular DivisionBrigham & Women’s HospitalBostonUSA
  2. 2.Harvard Medical SchoolBostonUSA
  3. 3.Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoCanada
  4. 4.Department of Molecular Genetics and MicrobiologyUniversity of TorontoTorontoCanada

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