Department of Genetics & Development, Columbia University Medical Center, New York, NY 10032, USA.
Database (Oxford). 2012 Apr 20;2012:bas022. doi: 10.1093/database/bas022. Print 2012.
Systematic biological screens typically identify many genes or proteins that are implicated in a specific phenotype. However, deriving mechanistic insight from these screens typically involves focusing upon one or a few genes within the set in order to elucidate their precise role in producing the phenotype. To find these critical genes, researchers use a variety of tools to query the set of genes to uncover underlying common genetic or physical interactions or common functional annotations (e.g. gene ontology terms). Not only it is necessary to find previous screens containing genes in common with the new set, but also useful to easily access the individual manuscript or study that classified those genes. Unfortunately, no tool currently exists to facilitate this task. We have developed a web-based tool (ScreenTroll) that queries one or more genes against a database of systematic yeast screens. The software determines which genome-wide yeast screens also identified the queried gene(s) and the resulting screens are listed in an order based on the extent of the overlap between the queried gene(s) and the open reading frames (ORFs) characterized in each individual yeast screen. In a separate list, the corresponding ORFs that are found in both the queried set of genes and each individual genome-wide screen are displayed along with links to the relevant manuscript via NIH's PubMed database. ScreenTroll is useful for comparing a list of ORFs with genes identified in a wide array of published genome-wide screens. This comparison informs users whether any of their queried ORFs overlaps a previous study in the ScreenTroll database. By listing the manuscript of the published screen, users can read more about the phenotype associated with that study. Together, this information provides insight into the function of the queried genes and helps the user focus on a subset of them.
系统生物学筛选通常会鉴定出许多与特定表型相关的基因或蛋白质。然而，从这些筛选中得出机制性的见解通常需要关注集合中的一个或几个基因，以阐明它们在产生表型中的精确作用。为了找到这些关键基因，研究人员使用各种工具来查询基因集，以揭示潜在的共同遗传或物理相互作用或共同的功能注释（例如基因本体术语）。不仅需要找到与新集合具有共同基因的先前筛选，而且还需要方便地访问将这些基因分类的单个手稿或研究。不幸的是，目前没有工具可以方便地完成这项任务。我们开发了一种基于网络的工具（ScreenTroll），可以针对系统酵母筛选数据库查询一个或多个基因。该软件确定哪些全基因组酵母筛选也鉴定了查询的基因，并根据查询基因与每个单独酵母筛选中鉴定的开放阅读框（ORF）之间的重叠程度，按顺序列出筛选结果。在另一个列表中，列出了在查询基因集和每个全基因组筛选中都找到的相应 ORF，并通过 NIH 的 PubMed 数据库链接到相关手稿。ScreenTroll 可用于比较广泛的已发表全基因组筛选中鉴定的基因列表和 ORF 列表。这种比较会通知用户他们查询的 ORF 是否与 ScreenTroll 数据库中的先前研究重叠。通过列出已发表屏幕的手稿，用户可以阅读更多关于该研究相关表型的信息。这些信息一起提供了有关查询基因功能的深入了解，并帮助用户专注于其中的一部分。
