Schlingemann Joerg, Habtemichael Negusse, Ittrich Carina, Toedt Grischa, Kramer Heidi, Hambek Markus, Knecht Rainald, Lichter Peter, Stauber Roland, Hahn Meinhard
1Division of Molecular Genetics, Deutsches Krebsforschungszentrum, Heidelberg, Germany.
Lab Invest. 2005 Aug;85(8):1024-39. doi: 10.1038/labinvest.3700293.
The comparison of gene expression measurements obtained with different technical approaches is of substantial interest in order to clarify whether inter-platform differences may conceal biologically significant information. To address this concern, we analyzed gene expression in a set of head and neck squamous cell carcinoma patients, using both spotted oligonucleotide microarrays made from a large collection of 70-mer probes and commercial arrays produced by in situ synthesis of sets of multiple 25-mer oligonucleotides per gene. Expression measurements were compared for 4425 genes represented on both platforms, which revealed strong correlations between the corresponding data sets. Of note, a global tendency towards smaller absolute ratios was observed when using the 70-mer probes. Real-time quantitative reverse transcription PCR measurements were conducted to verify expression ratios for a subset of genes and achieved good agreement regarding both array platforms. In conclusion, similar profiles of relative gene expression were obtained using arrays of either single 70-mer or multiple short 25-mer oligonucleotide probes per gene. Although qualitative assessments of the expression of individual genes have to be made with caution, our results indicate that the comparison of gene expression profiles generated on these platforms will help to discover disease-related gene signatures in general.
为了弄清楚不同平台间的差异是否会掩盖生物学上的重要信息，对采用不同技术方法获得的基因表达测量结果进行比较具有重大意义。为了解决这一问题，我们分析了一组头颈鳞状细胞癌患者的基因表达，使用了由大量70聚体探针制成的点阵寡核苷酸微阵列以及通过原位合成每个基因的多组25聚体寡核苷酸所生产的商业阵列。对两个平台上均有的4425个基因的表达测量结果进行比较，结果显示相应数据集之间存在很强的相关性。值得注意的是，使用70聚体探针时观察到绝对比值整体有变小的趋势。进行了实时定量逆转录PCR测量以验证一部分基因的表达比值，两个阵列平台在这方面达成了良好的一致性。总之，使用每个基因由单个70聚体或多个短25聚体寡核苷酸组成的阵列获得了相似的相对基因表达谱。尽管对单个基因表达的定性评估必须谨慎进行，但我们的结果表明，在这些平台上生成的基因表达谱的比较总体上将有助于发现与疾病相关的基因特征。
