The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA.
G3 (Bethesda). 2013 Aug 7;3(8):1335-40. doi: 10.1534/g3.113.006585.
The genome of budding yeast (Saccharomyces cerevisiae) contains approximately 5800 protein-encoding genes, the majority of which are associated with some known biological function. Yet the extent of amino acid sequence conservation of these genes over all phyla has only been partially examined. Here we provide a more comprehensive overview and visualization of the conservation of yeast genes and a means for browsing and exploring the data in detail, down to the individual yeast gene, at http://yeast-phylogroups.princeton.edu. We used data from the OrthoMCL database, which has defined orthologs from approximately 150 completely sequenced genomes, including diverse representatives of the archeal, bacterial, and eukaryotic domains. By clustering genes based on similar patterns of conservation, we organized and visualized all the protein-encoding genes in yeast as a single heat map. Most genes fall into one of eight major clusters, called "phylogroups." Gene ontology analysis of the phylogroups revealed that they were associated with specific, distinct trends in gene function, generalizations likely to be of interest to a wide range of biologists.
酿酒酵母（Saccharomyces cerevisiae）的基因组包含大约 5800 个编码蛋白质的基因，其中大多数与某些已知的生物学功能有关。然而，这些基因在所有门中的氨基酸序列保守程度仅得到了部分研究。在这里，我们提供了一个更全面的酵母基因保守性的概述和可视化，并提供了一种浏览和详细探索数据的方法，甚至可以深入到单个酵母基因，网址是 http://yeast-phylogroups.princeton.edu。我们使用了来自 OrthoMCL 数据库的数据，该数据库定义了来自大约 150 个完全测序的基因组的直系同源物，包括古菌、细菌和真核生物域的各种代表。通过基于相似的保守模式对基因进行聚类，我们将酵母中的所有编码蛋白质基因组织并可视化成一个单一的热图。大多数基因属于八个主要聚类之一，称为“ phylogroups”。对 phylogroups 的基因本体论分析表明，它们与基因功能的特定、独特趋势相关，这些概括可能对广泛的生物学家都有兴趣。
