Long versus short oligonucleotide microarrays for the study of gene expression in nonhuman primates
Long versus short oligonucleotide microarrays for the study of gene expression in nonhuman primates
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DOI：
10.1016/j.jneumeth.2005.09.007
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发表时间：
2006-04-15
影响因子：
3
通讯作者：
Hellmann, GM
中科院分区：
文献类型：
--
作者：
Walker, SJ;Wang, YL;Hellmann, GM
人类和非人类灵长类动物（NHP）基因组DNA之间的高度序列相似性表明，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，使用两种不同的商业上可获得的人类基因组微阵列平台，利用人类基因组U133 A基因芯片的AffytoHG U133 A基因芯片系统和利用人类基因组调查微阵列的应用生物系统表达阵列系统，来鉴定和表征人类酒精中毒的猕猴模型的前小脑中的基因表达变化。Affytek微阵列由每个基因的11个短寡核苷酸探针组组成，而Applied Biosystems微阵列每个基因使用单个长寡核苷酸。探针的交叉作图揭示了两个微阵列平台上共有11，542个基因。在这些常见的基因靶标中，小脑RNA样品的基因表达（“present calls”）的绝对测量值为65-70%（Applied Biosystems Expression Array System）和27-30%（AffymetrixGeneChip（R）System）。方差分析（ANOVA; p < 0.05;> 1.2倍变化;在至少50%的阵列上检测到的基因）分别表明应用生物系统和Affyssin微阵列的932和515个差异表达基因。微阵列的显著性分析（SAM）对于Applied Biosystems数据集以5%错误发现率（FDR）鉴定了255个显著基因，并且对于Affyssin数据集以60%FDR（最小FDR）鉴定了5个显著基因。基于TaqMan（R）分析的实时PCR对许多差异表达基因的验证产生的结果在大多数比较中与阵列数据一致。这项研究表明，人类序列为基础的DNA阵列可以有效地用于检测差异基因表达的NHP疾病模型，并提供证据表明，使用这种长的寡核苷酸为基础的微阵列平台可能更适合于跨物种的基因表达研究比短的基于谷胱甘肽的系统。(c)2005 Elsevier B. V.保留所有权利。
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 (R) System utilizing Human Genome U133A GeneChips (R) 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 (R) 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 (R) 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. (c) 2005 Elsevier B.V. All rights reserved.