Probe Selection and Expression Index Computation of Affymetrix Exon Arrays
Probe Selection and Expression Index Computation of Affymetrix Exon Arrays
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DOI：
10.1371/journal.pone.0000088
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发表时间：
2006-12-20
期刊：
影响因子：
3.7
通讯作者：
Wong, Wing Hung
中科院分区：
文献类型：
--
作者：
Xing, Yi;Kapur, Karen;Wong, Wing Hung
背景。目前人们对开发在基因水平和外显子水平上测量mRNA丰度的微阵列平台有着极大的兴趣。Affymetrix外显子阵列是一种新的高密度基因表达微阵列平台，拥有超过600万个针对基因组中所有已注释和预测外显子的探针。外显子阵列数据分析的一个重要问题是如何计算总体基因表达指数。由于外显子阵列探针设计的复杂性，这个问题在本质上不同于从传统的3′表达阵列中总结基因水平的表达。
方法/主要发现。在本文中，我们使用来自11种人类组织的外显子阵列数据来研究计算基因水平表达的方法。我们表明，对于大多数基因，存在一个外显子阵列探针子集，其在多个样本中的强度具有高度相关性。我们认为这些探针可作为总体基因表达水平的可靠指标。我们开发了一种探针选择算法，为每个基因选择这样一个高度相关的探针子集，并使用所选探针计算基因表达指数。
结论/意义。我们的结果表明，探针选择提高了从外显子阵列得到的基因表达估计值。所选探针可用于未来对其他外显子阵列数据集的分析，以计算基因表达指数。
Background. There is great current interest in developing microarray platforms for measuring mRNA abundance at both gene level and exon level. The Affymetrix Exon Array is a new high-density gene expression microarray platform, with over six million probes targeting all annotated and predicted exons in a genome. An important question for the analysis of exon array data is how to compute overall gene expression indexes. Because of the complexity of the design of exon array probes, this problem is different in nature from summarizing gene-level expression from traditional 39 expression arrays. Methodology/Principal Findings. In this manuscript, we use exon array data from 11 human tissues to study methods for computing gene-level expression. We showed that for most genes there is a subset of exon array probes having highly correlated intensities across multiple samples. We suggest that these probes could be used as reliable indicators of overall gene expression levels. We developed a probe selection algorithm to select such a subset of highly correlated probes for each gene, and computed gene expression indexes using the selected probes. Conclusions/Significance. Our results demonstrate that probe selection improves gene expression estimates from exon arrays. The selected probes can be used in future analyses of other exon array datasets to compute gene expression indexes.