Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach
Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach
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DOI：
10.1016/j.ygeno.2004.11.004
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发表时间：
2005-03-01
期刊：
影响因子：
4.4
通讯作者：
Buetow, KH
中科院分区：
文献类型：
--
作者：
Zhang, JH;Finney, RP;Buetow, KH
高密度寡核苷酸阵列已成为一种流行的检测方法，用于在基因组规模上同时测量mRNA表达。大量的努力致力于统计分析工具的开发，旨在减少实验噪音和规范化基因表达分析中的实验变异。然而，这些研究没有检测或编目与特定寡核苷酸探针相关的系统性问题。在这里，我们提出了一个有问题的探针，在多个实验中产生一致但不准确的信号的调查。通过评估基因、探针序列和基因组结构之间的数据完整性，我们确定了总共20，696个（10.5%）可以与多个基因交叉杂交的非特异性探针，以及总共18，363个（9.3%）在AffytechnologyGeneChip U95A/Av2阵列上错过靶转录物序列的探针。U133A阵列上的非特异性探针和错标探针的数量分别为29，405（12.1%）和19，717（8.0%）。在两个基因芯片实验中证实了错误标记的探针的不良性能，其中这些探针与正常探针相比在检测当前信号时显示出20 - 30%的降低。从SAGE和EST数据获得的定性表达信号与那些从基因芯片阵列的比较表明，两个平台的一致性是30%，低于在正常探针的问题探针。开发了一个Web应用程序来应用我们的结果，以提高表达分析的准确性。(c)2004年爱思唯尔公司All rights reserved.
High-density oligonucleotide arrays have become a popular assay for concurrent measurement of mRNA expression at the genome scale. Much effort has been devoted to the development of statistical analysis tools aimed at reducing experimental noise and normalizing experimental variation in gene expression analysis. However, these investigations do not detect or catalog systematic problems associated with specific oligonucleotide probes. Here, we present an investigation of problematic probes that yield consistent but inaccurate signals across multiple experiments. By evaluating data integrity among gene, probe sequence, and genomic structure we identified a total of 20,696 (10.5%) nonspecific probes that could cross-hybridize to multiple genes and a total of 18,363 (9.3%) probes that miss the target transcript sequences on the Affymetrix GeneChip U95A/Av2 array. The numbers of nonspecific and mistargeted probes on the U133A array are 29,405 (12.1%) and 19,717 (8.0%), respectively. The poor performance of the mistargeted probes was confirmed in two GeneChip experiments, in which these probes showed a 20-30% decrease in detecting present signals compared with normal probes. Comparison of qualitative expression signals obtained from SAGE and EST data with those from GeneChip arrays showed that the consistency of the two platforms is 30% lower in problematic probes than in normal probes. A Web application was developed to apply our results for improving the accuracy of expression analysis. (c) 2004 Elsevier Inc. All rights reserved.