Independence and reproducibility across microarray platforms
Independence and reproducibility across microarray platforms
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DOI：
10.1038/nmeth757
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发表时间：
2005-05-01
期刊：
影响因子：
48
通讯作者：
Quackenbush, J
中科院分区：
文献类型：
--
作者：
Larkin, JE;Frank, BC;Quackenbush, J
微阵列已被广泛用于基因表达的分析，但跨平台的可重复性问题尚未完全解决。为了解决这一明显的问题，我们比较了两个微阵列平台之间的基因表达：短的寡核苷酸Affyoung小鼠基因组430 2.0基因芯片和斑点cDNA阵列使用血管紧张素II诱导的高血压的小鼠模型。使用Affytek和cDNA平台分析从处理的小鼠提取的RNA，然后通过定量RT-PCR（qRT-PCR）验证特定基因。对于两个阵列上存在的11，710个基因，我们评估了实验处理和平台对测量表达的相对影响，发现生物处理对超过90%的基因的测量表达的影响远远大于平台，这一结果通过qRT-PCR验证。在平台产生不一致结果的少数情况下，qRT-PCR通常不能确认任何一组数据，这表明序列特异性效应可能使表达预测难以使用任何技术进行。
Microarrays have been widely used for the analysis of gene expression, but the issue of reproducibility across platforms has yet to be fully resolved. To address this apparent problem, we compared gene expression between two microarray platforms: the short otigonucleotide Affymetrix Mouse Genome 430 2.0 GeneChip and a spotted cDNA array using a mouse model of angiontensin II-induced hypertension. RNA extracted from treated mice was analyzed using Affymetrix and cDNA platforms and then by quantitative RT-PCR (qRT-PCR) for validation of specific genes. For the 11,710 genes present on both arrays, we assessed the relative impact of experimental treatment and platform on measured expression and found that biological treatment had a far greater impact on measured expression than did platform for more than 90% of genes, a result validated by qRT-PCR. In the small number of cases in which platforms yielded discrepant results, qRT-PCR generally did not confirm either set of data, suggesting that sequence-specific effects may make expression predictions difficult to make using any technique.