Sequencing of plant genomes is proceeding rapidly; and in the near future, genome sequences of a number of plant species will be available. While this will constitute a wealth of information, gaining deeper understanding of biological processes will require integrating functional genomics, proteomics, and interactomics data. For protein expression at the proteome scale, the systematic and comprehensive cloning of full-length ORFs in a standardized way will be required. Such ORFeome projects are initiated, and these resources will greatly enhance the possibilities in large-scale plant protein interaction mapping. Recent data suggest that interactome structures can be conserved between species and can therefore be instrumental in knowledge transfer and annotating protein functions across species. The availability of interactome data for several plant species will pave the way for such comparative approaches. High-throughput protein interaction data obtained with the Y2H system or likewise with MS approaches do not provide much information on the question of where and when proteins interact in vivo. The integration of interactome data with information from different resources such as expression profiles and phenotypic data have proven to effectively complement one another in predicting cellular functions. However, new concepts and most likely new technologies will be needed to proceed from the static picture of networks to the highly dynamic situation in vivo.
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