Comparison of nasal epithelial smoking-induced gene expression on Affymetrix Exon 1.0 and Gene 1.0 ST arrays.
Comparison of nasal epithelial smoking-induced gene expression on Affymetrix Exon 1.0 and Gene 1.0 ST arrays.
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Affymetrix Exon 1.0 和 Gene 1.0 ST 阵列上鼻上皮吸烟诱导的基因表达比较。
DOI：
10.1155/2013/951416
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发表时间：
2013
影响因子：
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通讯作者：
Spira,Avrum
中科院分区：
文献类型：
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作者：
Zhang,Xiaoling;Lenburg,MarcE;Spira,Avrum
我们先前已经使用Affytek Exon 1.0 ST阵列确定了吸烟对鼻上皮基因表达的影响。在这篇论文中，我们比较了Affyssin GeneChip Human Gene 1.0 ST阵列与Human Exon 1.0 ST阵列检测鼻吸烟相关基因表达变化的性能。从五个当前吸烟者和五个从不吸烟者的鼻上皮收集的RNA与两个阵列杂交。 虽然每个阵列平台内的样本间相关性在基因阵列中比在外显子阵列中相对更高，但大多数受吸烟影响最大的基因在平台之间紧密相关。尽管两个阵列数据集都不能以<0.05的错误发现率（FDR）检测差异表达基因（DEG），但我们使用Gene ST阵列偶然地鉴定了比预期更多的DEG。这些发现表明，虽然两个平台在检测吸烟诱导的差异基因表达变化方面表现出高度相关性，但Gene ST阵列可能是临床环境中基因水平全基因组表达谱分析的更具成本效益的平台，也是探索宿主对吸烟和其他吸入毒素反应的有效工具。
We have previously defined the impact of tobacco smoking on nasal epithelium gene expression using Affymetrix Exon 1.0 ST arrays. In this paper, we compared the performance of the Affymetrix GeneChip Human Gene 1.0 ST array with the Human Exon 1.0 ST array for detecting nasal smoking‐related gene expression changes. RNA collected from the nasal epithelium of five current smokers and five never smokers was hybridized to both arrays. While the intersample correlation within each array platform was relatively higher in the Gene array than that in the Exon array, the majority of the genes most changed by smoking were tightly correlated between platforms. Although neither array dataset was powered to detect differentially expressed genes (DEGs) at a false discovery rate (FDR) <0.05, we identified more DEGs than expected by chance using the Gene ST array. These findings suggest that while both platforms show a high degree of correlation for detecting smoking‐induced differential gene expression changes, the Gene ST array may be a more cost‐effective platform in a clinical setting for gene‐level genomewide expression profiling and an effective tool for exploring the host response to cigarette smoking and other inhaled toxins.