Larkin Jennie E, Frank Bryan C, Gavras Haralambos, Sultana Razvan, Quackenbush John
Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
Nat Methods. 2005 May;2(5):337-44. doi: 10.1038/nmeth757. Epub 2005 Apr 21.
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 oligonucleotide Affymetrix Mouse Genome 430 2.0 GeneChip and a spotted cDNA array using a mouse model of angiotensin 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.
微阵列已被广泛用于基因表达分析，但跨平台的可重复性问题尚未得到充分解决。为了解决这一明显问题，我们使用血管紧张素II诱导的高血压小鼠模型，比较了两个微阵列平台之间的基因表达：短寡核苷酸Affymetrix小鼠基因组430 2.0基因芯片和点阵cDNA阵列。从处理过的小鼠中提取的RNA使用Affymetrix和cDNA平台进行分析，然后通过定量逆转录聚合酶链反应（qRT-PCR）验证特定基因。对于两个阵列上都存在的11710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，发现对于超过90%的基因，生物处理对测量表达的影响远大于平台，这一结果通过qRT-PCR得到验证。在少数平台产生不一致结果的情况下，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使用任何技术进行表达预测都很困难。
