Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.
BACKGROUND
In the post-genomic era various functional genomics, proteomics and computational techniques have been developed to elucidate the protein interaction network. While some of these techniques are specific for a certain type of interaction, most predict a mixture of interactions. Qualitative labels are essential for the molecular biologist to experimentally verify predicted interactions.


RESULTS
Of the individual protein-protein interaction prediction methods, some can predict physical interactions without producing other types of interactions. None of the methods can specifically predict metabolic interactions. We have constructed an 'omics evidence landscape' that combines all sources of evidence for protein interactions from various types of omics data for Saccharomyces cerevisiae. We explore this evidence landscape to identify areas with either only metabolic or only physical interactions, allowing us to specifically predict the nature of new interactions in these areas. We combine the datasets in ways that examine the whole evidence landscape and not only the highest scoring protein pairs in both datasets and find specific predictions.


CONCLUSIONS
The combination of evidence types in the form of the evidence landscape allows for qualitative labels to be inferred and placed on the predicted protein interaction network of S. cerevisiae. These qualitative labels will help in the biological interpretation of gene networks and will direct experimental verification of the predicted interactions.
van Noort
Vera
V
Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Toernooiveld, 6525 ED Nijmegen, The Netherlands. Vera.vanNoort@embl.de
Snel
Berend
B
Huynen
Martijn A
MA
D000465:Algorithms; D000818:Animals; D001499:Bayes Theorem; D017173:Caenorhabditis elegans / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D004331:Drosophila melanogaster / Q000235:genetics; D005800:Genes, Fungal; D023281:Genomics / Q000379:methods / Q000592:standards; D006801:Humans; D011237:Predictive Value of Tests; D025941:Protein Interaction Mapping; D040901:Proteomics / Q000379:methods* / Q000592:standards*; D012044:Regression Analysis; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry
D029701:Saccharomyces cerevisiae Proteins