agriGO: a GO analysis toolkit for the agricultural community.
agriGO: a GO analysis toolkit for the agricultural community.
复制标题
agriGO：农业界的 GO 分析工具包
DOI：
10.1093/nar/gkq310
复制
发表时间：
2010-07
影响因子：
14.9
通讯作者：
Su Z
中科院分区：
文献类型：
--
作者：
Du Z;Zhou X;Ling Y;Zhang Z;Su Z
基因本体论(GO)是基因功能描述的事实标准，被广泛用于功能注释和丰富分析。在这里，我们介绍了agriGO，这是一个面向农业社区的基于Web的集成GO分析工具包，利用我们之前的GO丰富工具(EasyGO)的优势，满足新技术和研究目标的分析需求。EasyGO的精确度很高，事实证明，它在从高通量实验的海量数据集中发现生物知识方面很有用。对于agriGO，重新设计了系统架构和网站界面，以提高性能和可访问性。支持的生物和基因识别符得到了大幅扩展(包括由274个数据类型组成的38个农业物种)。对用户输入的要求更灵活，因为可以接受用户定义的引用和注释。此外，还提出了一种新的分析方法，使用了基因集丰富分析策略和可定制的特征。SEA、PAGE、BLAST4ID和SEACOMPARE四个工具被集成为一个工具包，以满足不同的需求。我们还提供交叉比较服务，以便以可视化的方式比较和探索不同的数据集。最后，agriGO作为一个具有搜索和下载功能的Go数据存储库；agriGO可在http://bioinfo.cau.edu.cn/agriGO/.上公开访问
Gene Ontology (GO), the de facto standard in gene functionality description, is used widely in functional annotation and enrichment analysis. Here, we introduce agriGO, an integrated web-based GO analysis toolkit for the agricultural community, using the advantages of our previous GO enrichment tool (EasyGO), to meet analysis demands from new technologies and research objectives. EasyGO is valuable for its proficiency, and has proved useful in uncovering biological knowledge in massive data sets from high-throughput experiments. For agriGO, the system architecture and website interface were redesigned to improve performance and accessibility. The supported organisms and gene identifiers were substantially expanded (including 38 agricultural species composed of 274 data types). The requirement on user input is more flexible, in that user-defined reference and annotation are accepted. Moreover, a new analysis approach using Gene Set Enrichment Analysis strategy and customizable features is provided. Four tools, SEA (Singular enrichment analysis), PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA), are integrated as a toolkit to meet different demands. We also provide a cross-comparison service so that different data sets can be compared and explored in a visualized way. Lastly, agriGO functions as a GO data repository with search and download functions; agriGO is publicly accessible at http://bioinfo.cau.edu.cn/agriGO/.
登录
查看更多内容
影响因子：
14.9
作者：
McCarthy FM;Bridges SM;Wang N;Magee GB;Williams WP;Luthe DS;Burgess SC
通讯作者：
Burgess SC
拟南芥信息资源（TAIR）：基因结构和功能注释。
影响因子：
14.9
作者：
Swarbreck, David;Wilks, Christopher;Lamesch, Philippe;Berardini, Tanya Z.;Garcia-Hernandez, Margarita;Foerster, Hartmut;Li, Donghui;Meyer, Tom;Muller, Robert;Ploetz, Larry;Radenbaugh, Amie;Singh, Shanker;Swing, Vanessa;Tissier, Christophe;Zhang, Peifen;Huala, Eva
通讯作者：
Huala, Eva
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：
14.9
作者：
Ouyang S;Zhu W;Hamilton J;Lin H;Campbell M;Childs K;Thibaud-Nissen F;Malek RL;Lee Y;Zheng L;Orvis J;Haas B;Wortman J;Buell CR
通讯作者：
Buell CR
影响因子：
14.9
作者：
Draghici, S;Khatri, P;Tainsky, MA
通讯作者：
Tainsky, MA