Platform influence on DNA microarray data in postmortem brain research
Platform influence on DNA microarray data in postmortem brain research
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DOI：
10.1016/j.nbd.2004.10.020
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发表时间：
2005-04-01
影响因子：
6.1
通讯作者：
Mirnics, K
中科院分区：
文献类型：
--
作者：
Hollingshead, D;Lewis, DA;Mirnics, K
除了人类之间的大量生物多样性之外，我们可靠地测量小幅度表达变化的能力有限，这显著降低了我们在死后大脑中获得收敛的转录组数据集的能力。特别是，微阵列平台的结构和灵敏度/再现性的差异，以及用于分析微阵列数据的各种工具，强烈影响实验结果。为了更好地理解三种常见DNA微阵列平台的灵敏度、动态范围和再现性，我们比较了两种人类死后样本在具有双荧光、寡核苷酸GeneChips（R）（Affyphase）和单色凝胶基质沉积的CodeLink（c）寡核苷酸阵列的cDNA微阵列上的情况。所有三个微阵列平台在重复实验中报告了良好的动态范围和高相关性，但它们未能一致地鉴定相同样品之间差异表达的相同基因。考虑到它们的可重复性和已被证明的准确性，不同的微阵列平台似乎根据其设计和功能的性质来测量不同的东西。在比较各项研究的数据时，需要考虑到这一点。(c)2004年爱思唯尔公司All rights reserved.
In addition to the substantial biological diversity among humans, our limited ability to reliably measure expression changes of small magnitude significantly reduces our capacity to obtain convergent sets of transcriptome data in postmortem brain. In particular, differences in the structure and sensitivity/reproducibility of microarray platforms, and in the variety of tools used to analyze microarray data, strongly influence experimental outcome. In order to better understand the sensitivity, dynamic range, and reproducibility of three common DNA microarray platforms, we compared two human postmortem samples on cDNA microarrays with dual-fluorescence, oligonucleotide GeneChips (R) (Affymetrix), and single-color gel matrix deposited CodeLink (c) oligonucleotide arrays. All three microarray platforms reported a good dynamic range and high correlation in replicate experiments, but they failed to consistently identify the same genes as differentially expressed between the same samples. Given their reproducibility and proven accuracy, different microarray platforms appear to be measuring different things by nature of their design and function. This needs to be taken into account when comparing data across studies. (c) 2004 Elsevier Inc. All rights reserved.