Rarely acting in isolation, it is invariably the physical associations among proteins that define their biological activity, necessitating the study of the cellular meshwork of protein-protein interactions (PPI) before a full appreciation of gene function can be achieved. The past few years have seen a marked expansion in the both the sheer volume and number of organisms for which high-quality interaction data is available, with high-throughput interaction screening and detection techniques showing consistent improvement both in scale and sensitivity. Although techniques for large-scale PPI mapping are increasingly being applied to new organisms, including human, there is a corresponding need to rigorously evaluate, benchmark, and impartially filter the results. This chapter explores methods for PPI dataset evaluation, including a survey of previous techniques applied by landmark studies in the field and a discussion of promising new experimental approaches. We further outline practical suggestions and useful tools for interpreting newly generated PPI data. As the majority of large-scale experimental data has been generated for the budding yeast S. cerevisiae, most of the techniques and datasets described are from the perspective of this model unicellular eukaryote; however, extensions to other organisms including mammals are mentioned where possible.
|Evidence ID||Analyze ID||Interactor||Interactor Systematic Name||Interactor||Interactor Systematic Name||Type||Assay||Annotation||Action||Modification||Phenotype||Source||Reference||Note|
|Evidence ID||Analyze ID||Gene||Gene Systematic Name||Gene Ontology Term||Gene Ontology Term ID||Qualifier||Aspect||Method||Evidence||Source||Assigned On||Reference||Annotation Extension|
|Evidence ID||Analyze ID||Gene||Gene Systematic Name||Phenotype||Experiment Type||Experiment Type Category||Mutant Information||Strain Background||Chemical||Details||Reference|
|Evidence ID||Analyze ID||Regulator||Regulator Systematic Name||Target||Target Systematic Name||Experiment||Conditions||Strain||Source||Reference|