Assessment of prediction accuracy of protein function from protein–protein interaction data

Abstract

Functional prediction of open reading frames coded in the genome is one of the most important tasks in yeast genomics. Among a number of large-scale experiments for assigning certain functional classes to proteins, experiments determining protein-protein interaction are especially important because interacting proteins usually have the same function. Thus, it seems possible to predict the function of a protein when the function of its interacting partner is known. However, in vitro experiments often suffer from artifacts and a protein can often have multiple binding partners with different functions. We developed an objective prediction method that can systematically include the information of indirect interaction. Our method can predict the subcellular localization, the cellular role and the biochemical function of yeast proteins with accuracies of 72.7%, 63.6% and 52.7%, respectively. The prediction accuracy rises for proteins with more than three binding partners and thus we present the open prediction results for 16 such proteins.

Involvement of Nst1p/YNL091w and Msl1p, a U2B″ splicing factor, in Saccharomyces cerevisiae salt tolerance

“…The fact that Nst1p interacts physically and genetically with Msl1p supports a direct participation in RNA processing. Inherent to this hypothesis, Nst1p should be a nuclear protein, something that is confirmed by computer-based prediction methods (Hishigaki et al, 2001). Unfortunately, we were not able to immunolocalize the protein, either with the GFP protein fused C-terminally, or with an N-terminal GST-tag.…”

Global protein function prediction from protein-protein interaction networks

“…Assigning to an unclassified protein the most common function(s) present among the classified interacting proteins, as in [7,8] (majority rule assignment) is rather straightforward. The majority rule relies on the empirical evidence that 70-80% of interacting proteins pairs share at least one function.…”

“…In this context, the search for reliable methods for proteins' function assignment is of uttermost importance. Previous approaches to deduce the unknown function of a class of proteins have exploited sequence similarities or clustering of co-regulated genes [2,3], phylogenetic profiles [4], protein-protein interactions [5,6,7,8], and protein complexes [9,10]. We propose to assign functional classes to proteins from their network of physical interactions, by minimizing the number of interacting proteins with different categories.…”

Protein Interactome and Its Application to Protein Function Prediction

“…After that, the Gibbs sampling technique is iteratively applied to determine the stable values of this probability for each protein. This approach resulted in higher performance than those of neighbourhood-based approaches (Chua et al, 2006;Hishigaki et al, 2001;Schwikowski et al, 2000) when utilized to the yeast PPI data.…”

“…However, this method lacked significance values for each association and the full network topology was not considered in the annotation process. A strategy was proposed to tackle the first problem of assigning statistical significance (Hishigaki et al, 2001). This was done by using 2…”