GeneTools--application for functional annotation and statistical hypothesis testing.
GeneTools--application for functional annotation and statistical hypothesis testing.
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DOI：
10.1186/1471-2105-7-470
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发表时间：
2006-10-24
影响因子：
3
通讯作者：
Laegreid A
中科院分区：
文献类型：
--
作者：
Beisvag V;Jünge FK;Bergum H;Jølsum L;Lydersen S;Günther CC;Ramampiaro H;Langaas M;Sandvik AK;Laegreid A
现代生物学已经从“一个基因”的方法转向基因组规模的分析方法，如微阵列技术，它允许同时测量数千个基因。这就产生了对便于以“批处理”模式解释生物数据的工具的需求。然而，这类工具往往给调查人员留下大量显然没有组织的信息。为了应对这一解释挑战，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一组基因中的生物信息。然而，该领域仍在发展，非常需要“综合”解决方案。GeneTools是一种网络服务，提供对数据库的访问，该数据库汇集了来自广泛资源的信息。注释数据每周更新一次，以保证用户获得最新可用的数据。用户提交的数据存储在数据库中，可以很容易地更新，在用户之间共享，并以各种格式导出。GeneTools提供三种不同的工具：i）NMC Annotation Tool，其以单次和批量搜索模式提供来自若干数据库（如UniGene、Genuz Gene、SwissProt和GeneOntology）的注释。ii）GO注释器工具，其中用户可以向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用于公共分发。iii）eGOn，用于GO类别表示的可视化和统计假设检验的工具。作为第一个GO工具，eGOn支持三种不同情况下的假设检验（主目标情况，互斥目标目标情况和交叉目标情况）。一个重要的附加功能是证据代码过滤器，允许用户选择GO注释进行分析。GeneTools是第一个“一体化”注释工具，为用户提供快速提取高度相关的基因注释数据，例如一次提取数千个基因或克隆。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。GeneTools可通过www.genetools.no免费获得
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
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影响因子：
5.8
作者：
Al-Shahrour, F;Díaz-Uriarte, R;Dopazo, J
通讯作者：
Dopazo, J
影响因子：
5.8
作者：
Hucka, M;Finney, A;Wang, J
通讯作者：
Wang, J
影响因子：
14.9
作者：
Draghici, S;Khatri, P;Tainsky, MA
通讯作者：
Tainsky, MA
DOI：
10.1073/pnas.96.6.2907
发表时间：
1999-03-16
影响因子：
11.1
作者：
Tamayo, P;Slonim, D;Golub, TR
通讯作者：
Golub, TR
影响因子：
14.9
作者：
Hull D;Wolstencroft K;Stevens R;Goble C;Pocock MR;Li P;Oinn T
通讯作者：
Oinn T