In recent years, significant technological developments have been achieved facilitating high-throughput protein interaction mapping that resulted in comprehensive protein interaction networks for a number of model organisms. Now eventually, medium- and large-scale protein interaction mapping projects are beginning to be established in plant research, and first results prove their value in revealing novel regulatory pathways and in dissecting the functions of uncharacterized proteins and protein families. Despite its inherent limitations and drawbacks, the Y2H system is the major source of comprehensive protein interaction data. With the accumulation of high-throughput data sets, the reliability of the data is increasingly becoming an issue. Here, knowledge from graph-theoretical analyses of interactome networks can be instrumental in revealing reliable and functionally significant patterns (functional modules, motifs or cliques) to direct focused experimental approaches aiming at a systems-level understanding of cellular functions.
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