Yeast Gene Ontology by Phenotypic Profiling

描述（申请人提供）：过去20年的研究表明，在面包酵母中，S。酿酒酵母，基本的细胞过程，以及执行它们的蛋白质，与人类细胞中的那些有很强的相似性。这提供了一个重要的手段，确定人类蛋白质的功能，通过他们的同源性，相互作用的伴侣，或与S的基因产物的功能相似性。酿酒酵母以及其他模式生物。然而，尽管面包酵母是大约八年前第一个被完全测序的真核生物，但仍然有大约30%的这种模式生物的基因功能未知。该提案的目标是通过对250种精心选择的所有非必需基因单独缺失的菌株进行敏感性的全基因组筛选，再加上对表型谱的复杂分析，来确定大量这些未表征基因的功能。我们的表型分析技术涉及PCR扩增的20个核苷酸的“条形码”，识别每个缺失菌株，高密度寡核苷酸阵列杂交。对任何处理的所得表型谱是敏感性的连续体，其允许对处理的表型谱进行比将表型“分箱”为敏感、正常和抗性的常见程序更准确的比较分析。我们已经用大约50种不同的治疗方法证明了表型谱的层次聚类是通过功能途径的相似性来聚类基因的有力方法。我们建议为生物界创造一种资源，使个人研究者能够询问我们的数据，以获得关于特定基因功能的假设，此外，还允许社区成员提出新的治疗方法，以帮助分配功能给单个基因。除了向社区提供表型分析数据和分析外，我们还将重点关注在DMA修复和染色质重塑中发现的新基因，并评估这些基因参与维持基因组稳定性的程度。

DESCRIPTION (provided by applicant): Research over the past 20 years has demonstrated that in Baker's yeast, S. cerevisiae, the basic cellular processes, and the proteins that carry them out, have strong similarities to those in human cells. This provides an important means of identifying the function of human proteins by their homologies, interacting partners, or similarities of function with the gene products of S. cerevisiae as well as other model organisms. However, despite the fact that Baker's yeast was the first eukaryote to be fully sequenced some eight years ago, there are still some 30% of the genes of this model organism whose function is unknown. The goal of this proposal is to identify the function of a large number of these uncharacterized genes by performing a genome-wide screen of the sensitivities to 250 carefully chosen treatments of strains with individual deletion of all non-essential genes, coupled with sophisticated analyses of the phenotypic profiles. Our phenotypic profiling technique involves hybridization of the PCR-amplified 20-nucleotide "barcodes" that identify each deletion strain, to high-density oligonucleotide arrays. The resulting phenotypic profile to any treatment is a continuum of sensitivity that allows more accurate comparative analyses of phenotypic profiles to the treatments than the common procedure of "binning" phenotypes into sensitive, normal, and resistant. We have demonstrated with some 50 different treatments that hierarchical clustering of the phenotypic profiles is a powerful method of clustering the genes by similarity of functional pathways . We propose to create for the biological community a resource that will allow individual investigators to interrogate our data for hypotheses as to the function of specific genes and, in addition, allow members of the community to suggest new treatments to aid in assigning function to individual genes. In addition to providing the phenotypic profiling data and analyses to the community, we will focus on new genes identified in DMA repair and chromatin remodeling and assess the extent to which these genes are involved in maintaining genome stability.