Wilder Steven P, Kaisaki Pamela J, Argoud Karène, Salhan Anita, Ragoussis Jiannis, Bihoreau Marie-Thérèse, Gauguier Dominique
The Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford, UK.
BMC Genomics. 2009 Feb 5;10:63. doi: 10.1186/1471-2164-10-63.
Microarray technologies are widely used to quantify the abundance of transcripts corresponding to thousands of genes. To maximise the robustness of transcriptome results, we have tested the performance and reproducibility of rat and mouse gene expression data obtained with Affymetrix, Illumina and Operon platforms.
We present a thorough analysis of the degree of reproducibility provided by analysing the transcriptomic profile of the same animals of several experimental groups under different popular microarray technologies in different tissues. Concordant results from inter- and intra-platform comparisons were maximised by testing many popular computational methods for generating fold changes and significances and by only considering oligonucleotides giving high expression levels. The choice of Affymetrix signal extraction technique was shown to have the greatest effect on the concordance across platforms. In both species, when choosing optimal methods, the agreement between data generated on the Affymetrix and Illumina was excellent; this was verified using qRT-PCR on a selection of genes present on all platforms.
This study provides an extensive assessment of analytical methods best suited for processing data from different microarray technologies and can assist integration of technologically different gene expression datasets in biological systems.
微阵列技术被广泛用于定量与数千个基因相对应的转录本丰度。为了使转录组结果的稳健性最大化，我们测试了使用Affymetrix、Illumina和Operon平台获得的大鼠和小鼠基因表达数据的性能和可重复性。
我们对在不同组织中使用不同流行微阵列技术分析几个实验组的相同动物的转录组图谱所提供的可重复性程度进行了全面分析。通过测试许多用于生成倍数变化和显著性的流行计算方法，并仅考虑表达水平高的寡核苷酸，平台间和平台内比较的一致结果得以最大化。结果表明，Affymetrix信号提取技术的选择对跨平台一致性影响最大。在两个物种中，选择最佳方法时，Affymetrix和Illumina上生成的数据之间的一致性非常好；这通过对所有平台上存在的一组基因进行qRT-PCR得到了验证。
本研究对最适合处理来自不同微阵列技术数据的分析方法进行了广泛评估，并有助于在生物系统中整合技术上不同的基因表达数据集。
