Hulsegge Ina, Kommadath Arun, Smits Mari A
Animal Breeding and Genomics Centre, Animal Sciences Group Wageningen UR, P,O, Box 65, 8200 AB Lelystad, The Netherlands.
BMC Proc. 2009 Jul 16;3 Suppl 4(Suppl 4):S10. doi: 10.1186/1753-6561-3-S4-S10.
Gene set analysis is a commonly used method for analysing microarray data by considering groups of functionally related genes instead of individual genes. Here we present the use of two gene set analysis approaches: Globaltest and GOEAST.Globaltest is a method for testing whether sets of genes are significantly associated with a variable of interest. GOEAST is a freely accessible web-based tool to test GO term enrichment within given gene sets. The two approaches were applied in the analysis of gene lists obtained from three different contrasts in a microarray experiment conducted to study the host reactions in broilers following Eimeria infection.
The Globaltest identified significantly associated gene sets in one of the three contrasts made in the microarray experiment whereas the functional analysis of the differentially expressed genes using GOEAST revealed enriched GO terms in all three contrasts.
Globaltest and GOEAST gave different results, probably due to the different algorithms and the different criteria used for evaluating the significance of GO terms.
基因集分析是一种常用的分析微阵列数据的方法，该方法通过考虑功能相关的基因组而非单个基因来进行分析。在此，我们展示两种基因集分析方法的应用：全局检验（Globaltest）和基因本体富集分析系统（GOEAST）。全局检验是一种用于检验基因集是否与感兴趣的变量显著相关的方法。基因本体富集分析系统是一个基于网络的免费工具，用于检验给定基因集内基因本体（GO）术语的富集情况。这两种方法应用于对从一项微阵列实验的三种不同对比中获得的基因列表进行分析，该实验旨在研究艾美耳球虫感染后肉鸡的宿主反应。
全局检验在微阵列实验的三种对比中的一种中鉴定出显著相关的基因集，而使用基因本体富集分析系统对差异表达基因进行功能分析时，在所有三种对比中均揭示了富集的基因本体术语。
全局检验和基因本体富集分析系统得出了不同的结果，这可能是由于不同的算法以及用于评估基因本体术语显著性的不同标准所致。
