Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate
Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate
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DOI：
10.1093/nar/gkg624
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发表时间：
2003-07-01
影响因子：
14.9
通讯作者：
Tainsky, MA
中科院分区：
文献类型：
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作者：
Draghici, S;Khatri, P;Tainsky, MA
Onto - Tools是一组四个无缝集成的数据库：Onto - Express、Onto - Compare、Onto - Design和Onto - Translate。Onto - Express能够将在特定条件下发现的差异调节基因列表自动转换为功能图谱，这些图谱描述了所研究的条件对各种生物过程和通路的影响。OE为以下类别构建功能图谱（使用基因本体术语）：生化功能、生物过程、细胞角色、细胞成分、分子功能和染色体位置。为每个类别计算统计显著性值。一旦初步的探索性分析确定了一些相关的生物过程，就可以对所研究的条件假设特定的相互作用机制。目前，有许多商业芯片可用于特定机制的研究。每个这样的芯片都有一个生物学偏差，该偏差由芯片上存在的基因代表特定通路的程度决定。Onto - Compare是一种工具，它可以对任何商业或定制芯片组进行高效比较。使用Onto - Compare，研究人员可以快速确定哪种芯片或哪组芯片最能涵盖所研究的假设。在许多情况下，没有针对特定生物学机制的商业芯片。Onto - Design是一种工具，它允许用户选择代表给定功能类别的基因。Onto - Translate允许用户轻松地将登录号列表、UniGene簇和Affymetrix探针相互转换。上述所有工具都是无缝集成的。Onto - Tools可在以下网址在线获取：>http://vortex.cs.wayne.edu/Projects.html
Onto-Tools is a set of four seamlessly integrated databases: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Onto-Express is able to automatically translate lists of genes found to be differentially regulated in a given condition into functional profiles characterizing the impact of the condition studied upon various biological processes and pathways. OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function and chromosome location. Statistical significance values are calculated for each category. Once the initial exploratory analysis identified a number of relevant biological processes, specific mechanisms of interactions can be hypothesized for the conditions studied. Currently, many commercial arrays are available for the investigation of specific mechanisms. Each such array is characterized by a biological bias determined by the extent to which the genes present on the array represent specific pathways. Onto-Compare is a tool that allows efficient comparisons of any sets of commercial or custom arrays. Using Onto-Compare, a researcher can determine quickly which array, or set of arrays, covers best the hypotheses studied. In many situations, no commercial arrays are available for specific biological mechanisms. Onto-Design is a tool that allows the user to select genes that represent given functional categories. Onto-Translate allows the user to translate easily lists of accession numbers, UniGene clusters and Affymetrix probes into one another. All tools above are seamlessly integrated. The Onto-Tools are available online at >http://vortex.cs.wayne.edu/Projects.html.