Information Center for Bio-Pharmacological Network, Seoul National University, Suwon 443-270, Korea.
BMC Bioinformatics. 2011 Feb 15;12 Suppl 1(Suppl 1):S25. doi: 10.1186/1471-2105-12-S1-S25.
Gene set analysis is a powerful method of deducing biological meaning for an a priori defined set of genes. Numerous tools have been developed to test statistical enrichment or depletion in specific pathways or gene ontology (GO) terms. Major difficulties towards biological interpretation are integrating diverse types of annotation categories and exploring the relationships between annotation terms of similar information.
GARNET (Gene Annotation Relationship NEtwork Tools) is an integrative platform for gene set analysis with many novel features. It includes tools for retrieval of genes from annotation database, statistical analysis & visualization of annotation relationships, and managing gene sets. In an effort to allow access to a full spectrum of amassed biological knowledge, we have integrated a variety of annotation data that include the GO, domain, disease, drug, chromosomal location, and custom-defined annotations. Diverse types of molecular networks (pathways, transcription and microRNA regulations, protein-protein interaction) are also included. The pair-wise relationship between annotation gene sets was calculated using kappa statistics. GARNET consists of three modules--gene set manager, gene set analysis and gene set retrieval, which are tightly integrated to provide virtually automatic analysis for gene sets. A dedicated viewer for annotation network has been developed to facilitate exploration of the related annotations.
GARNET (gene annotation relationship network tools) is an integrative platform for diverse types of gene set analysis, where complex relationships among gene annotations can be easily explored with an intuitive network visualization tool (http://garnet.isysbio.org/ or http://ercsb.ewha.ac.kr/garnet/).
基因集分析是一种从先验定义的基因集中推断生物学意义的强大方法。已经开发了许多工具来测试特定途径或基因本体 (GO) 术语中的统计丰度或耗竭。生物解释的主要困难是整合不同类型的注释类别并探索具有相似信息的注释术语之间的关系。
GARNET（基因注释关系网络工具）是一个具有许多新功能的基因集分析综合平台。它包括从注释数据库中检索基因、注释关系的统计分析和可视化以及管理基因集的工具。为了允许访问积累的各种生物学知识，我们整合了各种注释数据，包括 GO、域、疾病、药物、染色体位置和自定义定义的注释。还包括各种类型的分子网络（途径、转录和 microRNA 调节、蛋白质-蛋白质相互作用）。使用 Kappa 统计计算注释基因集之间的成对关系。GARNET 由三个模块组成——基因集管理器、基因集分析和基因集检索，它们紧密集成在一起，为基因集提供几乎自动的分析。开发了专门的注释网络查看器，以方便探索相关注释。
GARNET（基因注释关系网络工具）是一个用于多种类型的基因集分析的综合平台，其中可以使用直观的网络可视化工具轻松探索基因注释之间的复杂关系 (http://garnet.isysbio.org/ 或 http://ercsb.ewha.ac.kr/garnet/)。
