Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada.
Nat Protoc. 2010 Jun;5(6):1148-59. doi: 10.1038/nprot.2010.78. Epub 2010 Jun 3.
ErmineJ is software for the analysis of functionally interesting patterns in large gene lists drawn from gene expression profiling data or other high-throughput genomics studies. It can be used by biologists with no bioinformatics background to conduct sophisticated analyses of gene sets with multiple methods. It allows users to assess whether microarray data or other gene lists are enriched for a particular pathway or gene class. This protocol provides steps on how to format data files, determine analysis type, create custom gene sets and perform specific analyses-including overrepresentation analysis, genes score resampling and correlation resampling. ErmineJ differs from other methods in providing a rapid, simple and customizable analysis, including high-level visualization through its graphical user interface and scripting tools through its command-line interface, as well as custom gene sets and a variety of statistical methods. The protocol should take approximately 1 h, including (one-time) installation and setup.
ErmineJ 是一款用于分析从基因表达谱数据或其他高通量基因组学研究中提取的大型基因列表中功能有趣模式的软件。它可以供没有生物信息学背景的生物学家使用，通过多种方法对基因集进行复杂的分析。它允许用户评估微阵列数据或其他基因列表是否富集了特定的途径或基因类别。本方案提供了如何格式化数据文件、确定分析类型、创建自定义基因集和执行特定分析（包括过表达分析、基因评分重采样和相关重采样）的步骤。ErmineJ 与其他方法的不同之处在于提供了快速、简单和可定制的分析，包括通过其图形用户界面进行高级可视化以及通过其命令行界面进行脚本工具，以及自定义基因集和各种统计方法。该方案大约需要 1 小时，包括（一次性）安装和设置。
