Walker Stephen J, Wang Yulei, Grant Kathleen A, Chan Frances, Hellmann Gary M
Center for the Neurobehavioral Study of Alcohol, Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA.
J Neurosci Methods. 2006 Apr 15;152(1-2):179-89. doi: 10.1016/j.jneumeth.2005.09.007. Epub 2005 Oct 25.
The high degree of sequence similarity between human and nonhuman primate (NHP) genomic DNA suggests that human genome sequence-based DNA microarrays may be used effectively to study gene expression in NHP disease models. In the present study, two distinct commercially available human genome microarray platforms, the Affymetrix HG U133A GeneChip System utilizing Human Genome U133A GeneChips and the Applied Biosystems Expression Array System utilizing the Human Genome Survey Microarray, were used to identify and characterize gene expression changes in the anterior cerebellum of a macaque monkey model of human alcoholism. The Affymetrix microarray consists of eleven short oligonucleotide probe sets for each gene while the Applied Biosystems Microarray uses a single long oligonucleotide per gene. Cross-mapping of probes revealed a total of 11,542 genes that are represented on both microarray platforms. Absolute measures of gene expression ("present calls") from the cerebellum RNA samples were 65-70% (Applied Biosystems Expression Array System) and 27-30% (AffymetrixGeneChip System) among these common gene targets. Analysis of variance (ANOVA; p<0.05; >1.2 fold change; detected on at least 50% of the arrays) indicated 932 and 515 differentially expressed genes for the Applied Biosystems and Affymetrix microarrays, respectively. Significance analysis of microarrays (SAM) identified 255 significant genes at 5% false discovery rate (FDR) for the Applied Biosystems data set and five significant genes at 60% FDR (minimum FDR) for the Affymetrix data set. TaqMan assay-based real-time PCR validation of a number of differentially-expressed genes yielded results that agreed well with the array data in the majority of comparisons. This study demonstrates that human sequence-based DNA arrays can be used effectively to detect differential gene expression in an NHP disease model and provides evidence that the use of this long oligonucleotide-based microarray platform may be more suitable for cross-species gene expression studies than a short oligonucleotide-based system.
人类与非人类灵长类动物（NHP）基因组DNA之间高度的序列相似性表明，基于人类基因组序列的DNA微阵列可有效地用于研究NHP疾病模型中的基因表达。在本研究中，使用了两种不同的市售人类基因组微阵列平台，即利用人类基因组U133A基因芯片的Affymetrix HG U133A基因芯片系统和利用人类基因组调查微阵列的Applied Biosystems表达阵列系统，来鉴定和表征人类酒精中毒猕猴模型小脑中的基因表达变化。Affymetrix微阵列每个基因由11个短寡核苷酸探针集组成，而Applied Biosystems微阵列每个基因使用单个长寡核苷酸。探针的交叉映射显示，两个微阵列平台上共有11542个基因。在这些共同的基因靶点中，来自小脑RNA样本的基因表达绝对测量值（“存在呼叫”）在Applied Biosystems表达阵列系统中为65 - 70%，在Affymetrix基因芯片系统中为27 - 30%。方差分析（ANOVA；p<0.05；变化倍数>1.2；在至少50%的阵列上检测到）表明，Applied Biosystems和Affymetrix微阵列分别有932个和515个差异表达基因。微阵列显著性分析（SAM）在Applied Biosystems数据集的5%错误发现率（FDR）下鉴定出255个显著基因，在Affymetrix数据集的60% FDR（最小FDR）下鉴定出5个显著基因。基于TaqMan分析的实时PCR对一些差异表达基因的验证结果在大多数比较中与阵列数据非常吻合。本研究表明，基于人类序列的DNA阵列可有效地用于检测NHP疾病模型中的差异基因表达，并提供证据表明，与基于短寡核苷酸的系统相比，使用这种基于长寡核苷酸的微阵列平台可能更适合跨物种基因表达研究。
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