VSE knjižnice (vzajemna bibliografsko-kataložna baza podatkov COBIB.SI)
  • Geometric de-noising of protein-protein interaction networks
    Kuchaiev, Oleksii ...
    Understanding complex networks of protein-protein interactions (PPIs) is one of the foremost challenges of the postgenomic era. Due to the recent advances in experimental bio-technology, including ... yeast-2-hybrid (Y2H), tandem affinity purification (TAP) and other high-throughput methods for protein-protein interaction (PPI) detection, huge amounts of PPI network data are becoming available. Of major concern, however, are the levels of noise andincompleteness. For example, for Y2H screens, it is thought that the false positive rate could be as high as 64%, and the false negative rate may range from 43% to 71%. TAP experiments are believed to have comparable levels of noise. We present a novel technique to assess the confidence levels of interactions in PPI networks obtained from experimental studies. We use it forpredicting new interactions and thus for guiding future biological experiments. This technique is the first to utilize currently the best fittingnetwork model for PPI networks, geometric graphs. Our approach achievesspecificity of 85% and sensitivity of 90%. We use it to assign confidence scores to physical protein-protein interactions in the human PPI network downloaded from BioGRID. Using our approach, we predict 251 interactions in the human PPI network, a statistically significant fraction ofwhich correspond to protein pairs sharing common GO terms. Moreover, we validate a statistically significant portion of our predicted interactions in the HPRD database and the newer release of BioGRID. The data and Matlab code implementing the methods are freely available from the web site: http://www.kuchaev.com/Denoising.
    Vir: PLoS computational biology. - ISSN 1553-734X (Vol. 5, no. 8, 2009, str. 1-10)
    Vrsta gradiva - članek, sestavni del ; neleposlovje za odrasle
    Leto - 2009
    Jezik - angleški
    COBISS.SI-ID - 1024345409

    Povezava(-e):

    http://www.doc.ic.ac.uk/~natasha/journal%5b1%5d.pcbi.1000454.pdf

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