In silico prediction of physical protein interactions and characterization of interactome orphans

Max Kotlyar, Chiara Pastrello, Flavia Pivetta, Alessandra Lo Sardo, Christian Cumbaa, Han Li, Taline Naranian, Yun Niu, Zhiyong Ding, Fatemeh Vafaee, Fiona Broackes-Carter, Julia Petschnigg, Gordon B. Mills, Andrea Jurisicova, Igor Stagljar, Roberta Maestro, Igor Jurisica

    Research output: Contribution to journalArticle

    80 Scopus citations

    Abstract

    Protein-protein interactions (PPIs) are useful for understanding signaling cascades, predicting protein function, associating proteins with disease and fathoming drug mechanism of action. Currently, only a 1/410% of human PPIs may be known, and about one-third of human proteins have no known interactions. We introduce FpClass, a data mining-based method for proteome-wide PPI prediction. At an estimated false discovery rate of 60%, we predicted 250,498 PPIs among 10,531 human proteins; 10,647 PPIs involved 1,089 proteins without known interactions. We experimentally tested 233 high- and medium-confidence predictions and validated 137 interactions, including seven novel putative interactors of the tumor suppressor p53. Compared to previous PPI prediction methods, FpClass achieved better agreement with experimentally detected PPIs. We provide an online database of annotated PPI predictions (http://ophid.utoronto.ca/fpclass/) and the prediction software (http://www.cs.utoronto.ca/∼juris/data/fpclass/).

    Original languageEnglish (US)
    Pages (from-to)79-84
    Number of pages6
    JournalNature Methods
    Volume12
    Issue number1
    DOIs
    StatePublished - Jan 1 2014

    ASJC Scopus subject areas

    • Biotechnology
    • Biochemistry
    • Molecular Biology
    • Cell Biology

    Fingerprint Dive into the research topics of 'In silico prediction of physical protein interactions and characterization of interactome orphans'. Together they form a unique fingerprint.

  • Cite this

    Kotlyar, M., Pastrello, C., Pivetta, F., Lo Sardo, A., Cumbaa, C., Li, H., Naranian, T., Niu, Y., Ding, Z., Vafaee, F., Broackes-Carter, F., Petschnigg, J., Mills, G. B., Jurisicova, A., Stagljar, I., Maestro, R., & Jurisica, I. (2014). In silico prediction of physical protein interactions and characterization of interactome orphans. Nature Methods, 12(1), 79-84. https://doi.org/10.1038/nmeth.3178