PlantGSEA: a gene set enrichment analysis toolkit for plant community.
PlantGSEA: a gene set enrichment analysis toolkit for plant community.
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PlantGSEA：植物群落基因集富集分析工具包
DOI：
10.1093/nar/gkt281
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发表时间：
2013-07
影响因子：
14.9
通讯作者：
Su Z
中科院分区：
文献类型：
--
作者：
Yi X;Du Z;Su Z
基因集富集分析（Gene Set Enrichment Analysis，GSEA）是一种通过计算基因集与已知基因集的重叠来解释基因序列的生物学意义的有效方法。基因本体（GO）系统作为定义基因集合最广泛使用的注释之一，已被应用于许多富集分析工具中。EasyGO和agriGO是本实验室开发的两个GO富集分析工具包，自发布以来，由于其有效的性能和一致的维护，获得了广泛的使用和引用。为了满足用户对生物信息学分析的需求，我们开发了一个基于GSEA方法的植物生物信息学分析工具包PlantGSEA。在PlantGSEA中，收集了来自不同资源的20 290个定义的基因集并用于GSEA分析。PlantGSEA目前支持来自四种植物模型物种（拟南芥、水稻、玉米和雷蒙棉）的基因座ID和Affymatrix微阵列探针组ID。PlantGSEA是一个高效且用户友好的Web服务器，现在可以在http://structuralbiology.cau.edu.cn/PlantGSEA上公开访问。
Gene Set Enrichment Analysis (GSEA) is a powerful method for interpreting biological meaning of a list of genes by computing the overlaps with various previously defined gene sets. As one of the most widely used annotations for defining gene sets, Gene Ontology (GO) system has been used in many enrichment analysis tools. EasyGO and agriGO, two GO enrichment analysis toolkits developed by our laboratory, have gained extensive usage and citations since their releases because of their effective performance and consistent maintenance. Responding to the increasing demands of more comprehensive analysis from the users, we developed a web server as an important component of our bioinformatics analysis toolkit, named PlantGSEA, which is based on GSEA method and mainly focuses on plant organisms. In PlantGSEA, 20 290 defined gene sets deriving from different resources were collected and used for GSEA analysis. The PlantGSEA currently supports gene locus IDs and Affymatrix microarray probe set IDs from four plant model species (Arabidopsis thaliana, Oryza sativa, Zea mays and Gossypium raimondii). The PlantGSEA is an efficient and user-friendly web server, and now it is publicly accessible at http://structuralbiology.cau.edu.cn/PlantGSEA.
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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：
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：
Avraham, Shulamit;Tung, Chih-Wei;Ilic, Katica;Jaiswal, Pankaj;Kellogg, Elizabeth A.;McCouch, Susan;Pujar, Anuradha;Reiser, Leonore;Rhee, Seung Y.;Sachs, Martin M.;Schaeffer, Mary;Stein, Lincoln;Stevens, Peter;Vincent, Leszek;Zapata, Felipe;Ware, Doreen
通讯作者：
Ware, Doreen
agriGO：农业界的 GO 分析工具包
影响因子：
14.9
作者：
Du Z;Zhou X;Ling Y;Zhang Z;Su Z
通讯作者：
Su Z
影响因子：
14.9
作者：
Huang, Da Wei;Sherman, Brad T.;Lempicki, Richard A.
通讯作者：
Lempicki, Richard A.