在NCBI的基因表达综合数据库（GEO）中挖掘微阵列数据。
Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*.
作者信息
Barrett Tanya, Edgar Ron
机构信息
National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA.
出版信息
Methods Mol Biol. 2006;338:175-90. doi: 10.1385/1-59745-097-9:175.
Abstract
The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) has emerged as the leading fully public repository for gene expression data. This chapter describes how to use Web-based interfaces, applications, and graphics to effectively explore, visualize, and interpret the hundreds of microarray studies and millions of gene expression patterns stored in GEO. Data can be examined from both experiment-centric and gene-centric perspectives using user-friendly tools that do not require specialized expertise in microarray analysis or time-consuming download of massive data sets. The GEO database is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.
摘要
美国国立生物技术信息中心（NCBI）的基因表达综合数据库（GEO）已成为基因表达数据的主要完全公开存储库。本章介绍如何使用基于网络的界面、应用程序和图形来有效探索、可视化和解释存储在GEO中的数百项微阵列研究和数百万个基因表达模式。可以使用用户友好的工具从以实验为中心和以基因为中心的角度检查数据，这些工具不需要微阵列分析方面的专业知识，也无需耗时下载大量数据集。GEO数据库可通过万维网在http://www.ncbi.nlm.nih.gov/geo上公开访问。
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2
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3
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