Cross platform microarray analysis for robust identification of differentially expressed genes.
Cross platform microarray analysis for robust identification of differentially expressed genes.
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DOI：
10.1186/1471-2105-8-s1-s5
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发表时间：
2007-03-08
影响因子：
3
通讯作者：
Isacchi A
中科院分区：
文献类型：
--
作者：
Bosotti R;Locatelli G;Healy S;Scacheri E;Sartori L;Mercurio C;Calogero R;Isacchi A
微阵列已广泛用于基因表达分析，并且有几个商业平台可用。多个平台的组合使用可以克服每种方法的固有偏差，并且可以代表与RT-PCR互补的替代方案，用于鉴定基因表达谱中更稳健的变化。在本文中，我们结合统计和功能分析的跨平台验证的两个基于阿法替丁的技术，Affyphase（AFFX）和应用生物系统（ABI），并识别差异表达的基因。在这项研究中，我们分析了卵巢癌细胞系与细胞周期抑制剂治疗后差异表达的基因。分析处理的RNA与对照RNA在两个平台上代表的16425个基因的表达。我们使用CAT图评估了每个平台重复之间的重现性，我们发现两者都很高，AFFX的得分更高。然后，我们应用综合相关分析来评估研究中基因表达模式的可重复性，绕过了跨平台标准化表达测量的需要。我们确定了AFFX上930个差异表达基因和ABI上908个差异表达基因，两个平台约80%相同。尽管绝对值不同，但每个平台检测到的差异表达基因的强度范围相似。ABI的FC值的动态范围略高，这可能与其检测系统有关。62/66个差异表达基因经RT-PCR证实。在这项研究中，我们提出了一个跨平台验证的两个基于阿司那肽的技术，AFFX和ABI。我们发现重复之间具有良好的重现性，并表明两个平台都可用于选择差异表达的基因，且基本一致。受影响的功能的途径分析确定的主题与细胞周期抑制剂预期的一致，表明该程序适用于促进与化合物治疗相关的生物学相关特征的鉴定。对常见基因和平台特异性基因的高确认率表明，平台的组合可以克服与探针设计和技术特征相关的偏差，从而加速鉴定值得信赖的差异表达基因。
Microarrays have been widely used for the analysis of gene expression and several commercial platforms are available. The combined use of multiple platforms can overcome the inherent biases of each approach, and may represent an alternative that is complementary to RT-PCR for identification of the more robust changes in gene expression profiles. In this paper, we combined statistical and functional analysis for the cross platform validation of two oligonucleotide-based technologies, Affymetrix (AFFX) and Applied Biosystems (ABI), and for the identification of differentially expressed genes. In this study, we analysed differentially expressed genes after treatment of an ovarian carcinoma cell line with a cell cycle inhibitor. Treated versus control RNA was analysed for expression of 16425 genes represented on both platforms. We assessed reproducibility between replicates for each platform using CAT plots, and we found it high for both, with better scores for AFFX. We then applied integrative correlation analysis to assess reproducibility of gene expression patterns across studies, bypassing the need for normalizing expression measurements across platforms. We identified 930 genes as differentially expressed on AFFX and 908 on ABI, with ~80% common to both platforms. Despite the different absolute values, the range of intensities of the differentially expressed genes detected by each platform was similar. ABI showed a slightly higher dynamic range in FC values, which might be associated with its detection system. 62/66 genes identified as differentially expressed by Microarray were confirmed by RT-PCR. In this study we present a cross-platform validation of two oligonucleotide-based technologies, AFFX and ABI. We found good reproducibility between replicates, and showed that both platforms can be used to select differentially expressed genes with substantial agreement. Pathway analysis of the affected functions identified themes well in agreement with those expected for a cell cycle inhibitor, suggesting that this procedure is appropriate to facilitate the identification of biologically relevant signatures associated with compound treatment. The high rate of confirmation found for both common and platform-specific genes suggests that the combination of platforms may overcome biases related to probe design and technical features, thereby accelerating the identification of trustworthy differentially expressed genes.