Three microarray platforms: an analysis of their concordance in profiling gene expression.
Three microarray platforms: an analysis of their concordance in profiling gene expression.
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三个微阵列平台：对它们在分析基因表达的一致性的分析。
DOI：
10.1186/1471-2164-6-63
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发表时间：
2005-05-05
期刊：
影响因子：
4.4
通讯作者：
Kawasaki, ES
中科院分区：
文献类型：
--
作者：
Petersen, D;Chandramouli, GVR;Geoghegan, J;Hilburn, J;Paarlberg, J;Kim, CH;Munroe, D;Gangi, L;Han, J;Puri, R;Staudt, L;Weinstein, J;Barrett, JC;Green, J;Kawasaki, ES
用于基因表达分析的微阵列有三种不同的类型：短寡核苷酸(25-30碱基)、长寡核苷酸(50-80碱基)和cDNA(长度高度可变)。到目前为止，短寡核苷酸和cDNA阵列一直是表达分析的主流，但长寡核苷酸平台正在变得越来越受欢迎，并有可能取代cDNA阵列。作为长寡核苷酸阵列验证研究的一部分，我们比较和对比了三种形式的表达谱，对照通用参考标准测试了六种不同细胞系的RNA。这三个平台有6430个共同的基因。总的来说，当通过表达差异方向的一致性(上调或下调)、散点图分析、主成分分析、细胞系相关性或定量RT-PCR来定义时，跨平台的基因表达水平的相关性是好的。通过对散点图的分析，平台之间的总体相关性(r值)在0.7至0.8的范围内。当在p值为0.05和表达阈值水平为1.5倍和2倍时测量显著的表达比率的一致性时，平台之间的一致性非常高，从93%到100%。我们的结果表明，长寡核苷酸平台非常适合于表达分析，并且与cDNA型和短型寡核苷酸品种相比是有利的。如果标准是基因表达的变化方向，并且最小限度地强调变化的大小，那么这三个平台都可以给出类似的和可重复的结果。
Microarrays for the analysis of gene expression are of three different types: short oligonucleotide (25–30 base), long oligonucleotide (50–80 base), and cDNA (highly variable in length). The short oligonucleotide and cDNA arrays have been the mainstay of expression analysis to date, but long oligonucleotide platforms are gaining in popularity and will probably replace cDNA arrays. As part of a validation study for the long oligonucleotide arrays, we compared and contrasted expression profiles from the three formats, testing RNA from six different cell lines against a universal reference standard. The three platforms had 6430 genes in common. In general, correlation of gene expression levels across the platforms was good when defined by concordance in the direction of expression difference (upregulation or downregulation), scatter plot analysis, principal component analysis, cell line correlation or quantitative RT-PCR. The overall correlations (r values) between platforms were in the range 0.7 to 0.8, as determined by analysis of scatter plots. When concordance was measured for expression ratios significant at p-values of <0.05 and at expression threshold levels of 1.5 and 2-fold, the agreement among the platforms was very high, ranging from 93% to 100%. Our results indicate that the long oligonucleotide platform is highly suitable for expression analysis and compares favorably with the cDNA and short oligonucleotide varieties. All three platforms can give similar and reproducible results if the criterion is the direction of change in gene expression and minimal emphasis is placed on the magnitude of change.
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