One of the major goals of the emerging field of proteomics is the establishment of relationships between protein function and particular diseases. Proteomic technologies are used to try to identify important genes and their related proteins implicated in diseases and their treatments and to understand the role these genes and their related proteins play in the onset and progression of disease. A major proteomics challenge is to determine the set of proteins expressed in the cell and the interactions between such proteins, which in turn define the functional pathways of the cell. If a given pathway is linked to a disease, then the proteins within the pathway or a functionally related pathway may represent drug targets for treatment of the disease.
Accordingly, there is a need in the art for functional proteomics technologies which provide valuable functional information about genes encoding proteins with previously unknown roles. Yeast based proteomics represents one such technology. Functional genomics and proteomics strategies involving large-scale construction of defined mutants have created the potential for the systematic mapping of genetic interactions on a genome-wide scale. In addition to the recent sequencing of the human genome, the genomes of other, simpler, organisms have been completely sequenced, including that of the budding yeast Saccharomyces cerevesiae. For S. cerevisiae, deletion mutations have been constructed for all 6,200 suspected genes, identifying a set of approximately 1200 essential yeast genes and approximately 5,000 nonessential genes, resulting in approximately 5000 viable haploid gene deletion mutants. With genome sequence in hand, the monumental challenge is to understand the roles of the approximately 6,200 predicted yeast gene products. The scope of the challenge is immense. Approximately one-third of all predicted yeast genes are classified as coding for proteins of unknown function [Saccharomyces Genome Database (http://genome-www.stanford.edu/Saccharomyces/)]. Further, among a test pool of 558 homozygous deletion strains, over 60% had no observable growth defect after 60 generations. Simple extrapolation to more complex genomes suggests that the absence of obvious functions for a large fraction of encoded proteins will quickly become an enormous problem in biology.
There is a need, therefore, for proteomics technologies which can assess the previously unknown functions of proteins. The phenotypic analysis of the set of viable deletion strains within certain species of yeast represents a major challenge because the role of many genes will only be manifest under very specialized growth conditions. To address this problem, the present invention provides a high throughput method for the construction of yeast double-mutants that enables the phenotype associated with a specific mutation to be examined systematically within the context of thousands of different gene deletion backgrounds. A comprehensive application of this method will identify the precise genetic conditions under which each yeast gene is critical for fitness of the organism and may reveal a conserved network of genetic interactions linking fundamental processes and pathways of eukaryotic cells. Because many non-essential yeast genes have mammalian homologues systematic synthetic lethal analysis on yeast will provide crucial insights into the gene function problem in all eukaryotes. Such synthetic lethal analysis can be performed on the yeast arrays of the present invention. The high density yeast output arrays and the methods of analyzing such arrays of the present invention therefore fulfill a need in the art by providing simple and efficient methods for large-scale, high throughput analysis of genetic and protein-protein interactions.