D'mello Veera, Lee Ju Y, MacDonald Clinton C, Tian Bin
Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07101, USA.
Appl Bioinformatics. 2006;5(4):249-53. doi: 10.2165/00822942-200605040-00007.
DNA microarrays have been widely used to examine gene expression. The Affymetrix GeneChip is one of the most commonly used platforms, employing DNA probes of 25 nucleotides designed to hybridise to different regions of target mRNA. The targeted region is often biased toward the 3' end of mRNA, which can lead to biases in detection. A large number of mammalian genes can undergo alternative polyadenylation under different cellular conditions. Multiple polyadenylation sites can lead to variable transcripts with different hybridisation properties. Here, we surveyed probes on human, mouse and rat GeneChip arrays and found that the detection of a significant proportion of mRNAs can potentially be affected by alternative polyadenylation. This could lead to inaccurate interpretation of GeneChip data when the changes of expression values actually result from alternative use of polyadenylation sites.
DNA微阵列已被广泛用于检测基因表达。Affymetrix基因芯片是最常用的平台之一，它使用25个核苷酸的DNA探针，设计用于与靶mRNA的不同区域杂交。靶向区域通常偏向mRNA的3'端，这可能导致检测偏差。大量哺乳动物基因在不同细胞条件下可发生可变聚腺苷酸化。多个聚腺苷酸化位点可导致具有不同杂交特性的可变转录本。在这里，我们调查了人类、小鼠和大鼠基因芯片阵列上的探针，发现相当一部分mRNA的检测可能会受到可变聚腺苷酸化的潜在影响。当表达值的变化实际上是由聚腺苷酸化位点的交替使用引起时，这可能导致对基因芯片数据的错误解读。
