Beisvag Vidar, Jünge Frode K R, Bergum Hallgeir, Jølsum Lars, Lydersen Stian, Günther Clara-Cecilie, Ramampiaro Heri, Langaas Mette, Sandvik Arne K, Laegreid Astrid
Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
BMC Bioinformatics. 2006 Oct 24;7:470. doi: 10.1186/1471-2105-7-470.
Modern biology has shifted from "one gene" approaches to methods for genomic-scale analysis like microarray technology, which allow simultaneous measurement of thousands of genes. This has created a need for tools facilitating interpretation of biological data in "batch" mode. However, such tools often leave the investigator with large volumes of apparently unorganized information. To meet this interpretation challenge, gene-set, or cluster testing has become a popular analytical tool. Many gene-set testing methods and software packages are now available, most of which use a variety of statistical tests to assess the genes in a set for biological information. However, the field is still evolving, and there is a great need for "integrated" solutions.
GeneTools is a web-service providing access to a database that brings together information from a broad range of resources. The annotation data are updated weekly, guaranteeing that users get data most recently available. Data submitted by the user are stored in the database, where it can easily be updated, shared between users and exported in various formats. GeneTools provides three different tools: i) NMC Annotation Tool, which offers annotations from several databases like UniGene, Entrez Gene, SwissProt and GeneOntology, in both single- and batch search mode. ii) GO Annotator Tool, where users can add new gene ontology (GO) annotations to genes of interest. These user defined GO annotations can be used in further analysis or exported for public distribution. iii) eGOn, a tool for visualization and statistical hypothesis testing of GO category representation. As the first GO tool, eGOn supports hypothesis testing for three different situations (master-target situation, mutually exclusive target-target situation and intersecting target-target situation). An important additional function is an evidence-code filter that allows users, to select the GO annotations for the analysis.
GeneTools is the first "all in one" annotation tool, providing users with a rapid extraction of highly relevant gene annotation data for e.g. thousands of genes or clones at once. It allows a user to define and archive new GO annotations and it supports hypothesis testing related to GO category representations. GeneTools is freely available through www.genetools.no
现代生物学已从“单基因”方法转向基因组规模分析方法，如微阵列技术，该技术可同时测量数千个基因。这就需要有助于以“批量”模式解释生物学数据的工具。然而，这类工具往往会让研究人员面对大量看似杂乱无章的信息。为应对这一解释挑战，基因集或聚类测试已成为一种流行的分析工具。现在有许多基因集测试方法和软件包，其中大多数使用各种统计测试来评估集合中的基因的生物学信息。然而，该领域仍在不断发展，非常需要“集成”解决方案。
GeneTools是一项网络服务，可访问一个整合了来自广泛资源信息的数据库。注释数据每周更新，确保用户获取最新可用数据。用户提交的数据存储在数据库中，可轻松更新、在用户之间共享并以各种格式导出。GeneTools提供三种不同工具：i）NMC注释工具，它以单搜索和批量搜索模式提供来自多个数据库（如UniGene、Entrez Gene、SwissProt和基因本体论）的注释。ii）GO注释工具，用户可在其中为感兴趣的基因添加新的基因本体（GO）注释。这些用户定义的GO注释可用于进一步分析或导出以供公众使用。iii）eGOn，一种用于GO类别表示可视化和统计假设检验的工具。作为首个GO工具，eGOn支持针对三种不同情况（主-靶情况、相互排斥的靶-靶情况和相交的靶-靶情况）进行假设检验。一个重要的附加功能是证据代码过滤器，允许用户选择用于分析的GO注释。
GeneTools是首个“一体化”注释工具，可为用户快速提取例如数千个基因或克隆的高度相关基因注释数据。它允许用户定义和存档新的GO注释，并支持与GO类别表示相关的假设检验。可通过www.genetools.no免费获取GeneTools
