Arabidopsis transcript profiling on Affymetrix GeneChip arrays
Arabidopsis transcript profiling on Affymetrix GeneChip arrays
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DOI：
10.1023/b:plan.0000019069.23317.97
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发表时间：
2003-11-01
影响因子：
5.1
通讯作者：
Gruissem, W
中科院分区：
文献类型：
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作者：
Hennig, L;Menges, M;Gruissem, W
DNA微阵列正成为一种常用的研究工具。虽然几项研究已经证实了在重复阵列上分析相同RNA样品的可重复性，但是很少有对携带针对一组共同基因的不同探针的微阵列之间的转录物谱分析结果的可重复性的分析。为了解决这个问题，我们比较了植物研究中常用的两种微阵列的性能和再现性，包含超过8000个探针集的Affyphidopsis AG阵列和包含超过22000个重新设计的探针集的Affyphidopsis ATH1阵列。总共标记了21种不同的RNA样品，并与两种微阵列类型平行杂交。聚焦于两种阵列检测到的超过7300个目标的重叠，我们发现了高度的可重复性。尽管使用了不同的探针组，但对于大多数基因，信号和信号对数比都非常相似。然而，在MAS5.0中实施的Affysset '统计算法称为缺失或未改变的基因显示出相当少的表达模式保守性。此外，我们确定了大约300个基因，这些基因用两种微阵列产生了强烈不同的测量结果，强调RNA分析数据需要仔细解释。总体而言，本研究表明，使用ATH 1和AG阵列获得的结果非常相似，因此分析在很大程度上独立于探针集。然而，结果强调需要适当的过滤方案，如那些基于当前和改变由MAS 5.0提供的调用，而不是仅仅依赖于信号值。
DNA microarrays are becoming a frequently used research tool. Whilst several studies have confirmed the reproducibility of analysing the same RNA samples on duplicate arrays, there is little analysis of the reproducibility of the results of transcript profiling between microarrays carrying different probes to a common set of genes. To address this question, we compared the performance and reproducibility of two microarrays commonly used in plant research, the Affymetrix Arabidopsis AG array containing more than 8000 probe sets and the Affymetrix Arabidopsis ATH1 array containing more than 22 000 redesigned probe sets. A total of 21 different RNA samples were labelled and hybridized in parallel to the two microarray types. Focusing on the overlap of more than 7300 targets detected with both arrays, we found a high degree of reproducibility. Despite the use of different probe sets, both signal and signal log ratio were very similar for most genes. However, genes that were called absent or not changed by Affymetrix' statistical algorithm implemented in MAS5.0 showed considerably less conservation of expression patterns. Moreover, we identified about 300 genes that yielded strongly different measurements with the two microarrays, emphasizing that RNA profiling data need careful interpretation. Overall, this study shows that results obtained with ATH1 and AG arrays are very comparable and hence that the analysis is largely independent of probe sets. However, the result emphasize the need for appropriate filtering schemes such as those based on the present and change calls provided by MAS5.0 rather than reliance solely on signal values.