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Topological scoring of protein interaction networks

Author

Listed:
  • Mihaela E. Sardiu

    (Stowers Institute for Medical Research)

  • Joshua M. Gilmore

    (Stowers Institute for Medical Research
    Boehringer Ingelheim Vetmedica)

  • Brad D. Groppe

    (Stowers Institute for Medical Research
    Thermo Fisher Scientific)

  • Arnob Dutta

    (Stowers Institute for Medical Research
    University of Rhode Island)

  • Laurence Florens

    (Stowers Institute for Medical Research)

  • Michael P. Washburn

    (Stowers Institute for Medical Research
    The University of Kansas Medical Center)

Abstract

It remains a significant challenge to define individual protein associations within networks where an individual protein can directly interact with other proteins and/or be part of large complexes, which contain functional modules. Here we demonstrate the topological scoring (TopS) algorithm for the analysis of quantitative proteomic datasets from affinity purifications. Data is analyzed in a parallel fashion where a prey protein is scored in an individual affinity purification by aggregating information from the entire dataset. Topological scores span a broad range of values indicating the enrichment of an individual protein in every bait protein purification. TopS is applied to interaction networks derived from human DNA repair proteins and yeast chromatin remodeling complexes. TopS highlights potential direct protein interactions and modules within complexes. TopS is a rapid method for the efficient and informative computational analysis of datasets, is complementary to existing analysis pipelines, and provides important insights into protein interaction networks.

Suggested Citation

  • Mihaela E. Sardiu & Joshua M. Gilmore & Brad D. Groppe & Arnob Dutta & Laurence Florens & Michael P. Washburn, 2019. "Topological scoring of protein interaction networks," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-09123-y
    DOI: 10.1038/s41467-019-09123-y
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