Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles.
Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles.
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DOI：
10.1186/1471-2105-10-s11-s12
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发表时间：
2009-10-08
影响因子：
3
通讯作者：
Chen T
中科院分区：
文献类型：
--
作者：
Li Z;Su Z;Wen Z;Shi L;Chen T
几种不同的微阵列平台可用于测量基因表达。微阵列科学界对这些平台的平台内和平台间一致性存在分歧。在不同平台上，就具有显著差异表达的基因而言，证明了高和低的表达。基因表达的阵列研究用于探索生物学原因和影响。因此，最终应该在生物学环境中评估一致性，以揭示所检查的样品之间的功能差异，而不仅仅是差异表达基因（DEG）的列表。在这项研究中，我们调查了不同的平台是否具有高度的一致性，从生物功能的角度来看。将未过滤来自不同平台的微阵列中的不同探针的DEG数据输入到Incidity Pathway Analysis（IPA）系统中进行功能分析，所述微阵列来自五个测试点，所述五个测试点使用来自Affytron、Applied Biosystems、Agilent和GE health平台的微阵列（两个测试点使用Affytron进行平台内比较），所述微阵列来自用肾脏致癌物马兜铃酸处理的大鼠的肾脏样品。在四个不同的平台和Affyoung平台的两个测试中心之间比较了由IPA确定的DEG列表的功能。分析结果表明，使用同一平台的两个测试站点之间或不同平台之间存在非常高的一致性。不同平台确定的最高功能非常相似，反映了马兜铃酸在大鼠肾脏中的致癌性和毒性。我们的研究结果表明，高度一致的生物信息可以从不同的微阵列平台产生。
Several different microarray platforms are available for measuring gene expression. There are disagreements within the microarray scientific community for intra- and inter-platform consistency of these platforms. Both high and low consistencies were demonstrated across different platforms in terms of genes with significantly differential expression. Array studies for gene expression are used to explore biological causes and effects. Therefore, consistency should eventually be evaluated in a biological setting to reveal the functional differences between the examined samples, not just a list of differentially expressed genes (DEG). In this study, we investigated whether different platforms had a high consistency from the biologically functional perspective. DEG data without filtering the different probes in microarrays from different platforms generated from kidney samples of rats treated with the kidney carcinogen, aristolochic acid, in five test sites using microarrays from Affymetrix, Applied Biosystems, Agilent, and GE health platforms (two sites using Affymetrix for intra-platform comparison) were input into the Ingenuity Pathway Analysis (IPA) system for functional analysis. The functions of the DEG lists determined by IPA were compared across the four different platforms and two test sites for Affymetrix platform. Analysis results showed that there is a very high level of consistency between the two test sites using the same platform or among different platforms. The top functions determined by the different platforms were very similar and reflected carcinogenicity and toxicity of aristolochic acid in the rat kidney. Our results demonstrate that highly consistent biological information can be generated from different microarray platforms.