Statistical analysis of array expression data as applied to the problem of tamoxifen resistance
Statistical analysis of array expression data as applied to the problem of tamoxifen resistance
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DOI：
10.1093/jnci/91.5.453
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发表时间：
1999-03-03
期刊：
影响因子：
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通讯作者：
Fuqua, SAW
中科院分区：
文献类型：
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作者：
Hilsenbeck, SG;Friedrichs, WE;Fuqua, SAW
背景资料：尽管新兴的互补DNA（cDNA）阵列技术在识别基因表达的复杂模式方面有很大的希望，但其新奇意味着没有完善的标准来指导其产生的数据的分析和解释。我们已经使用由CLONTECH Atlas（TM）人类cDNA阵列产生的初步数据，通过研究乳腺癌中获得性他莫昔芬耐药性发展过程中基因表达的变化，开发了一种实用的方法来对这些数据进行统计分析。研究方法：为了与阵列杂交，我们从MCF-7人乳腺细胞肿瘤中制备了RNA，该肿瘤是从雌激素刺激、他莫昔芬敏感和他莫昔芬耐药生长期间获得性他莫昔芬耐药的无胸腺裸小鼠异种移植模型中分离出来的。主成分分析用于鉴定具有改变的表达的基因。结果与结论：主成分分析产生三个主成分，其被解释为1）基因表达的平均水平，2）雌激素刺激的基因表达与他莫昔芬敏感和他莫昔芬抗性基因表达的平均值之间的差异，以及3）他莫昔芬敏感和他莫昔芬抗性基因表达之间的差异。使用双变量（第二和第三主成分）99%预测区域来鉴定表现出改变的表达的离群基因。选择两个代表性的异常基因erk-2和HSF-1（热休克转录因子-1）进行验证性研究，并在western blot分析中证实其预测的相对表达水平，表明可以使用阵列技术进行半定量估计。含义：主成分分析提供了一个有用的和实用的方法来分析基因表达数据从cDNA阵列，该方法可以识别广泛的模式的表达变化，并基于一个小的模拟研究，将可能提供合理的权力，以检测中等大小的变化，在临床相关基因。
Background: Although the emerging complementary DNA (cDNA) array technology holds great promise to discern complex patterns of gene expression, its novelty means that there are no well-established standards to guide analysis and interpretation of the data that it produces. We have used preliminary data generated with the CLONTECH Atlas(TM) human cDNA array to develop a practical approach to the statistical analysis of these data by studying changes in gene expression during the development of acquired tamoxifen resistance in breast cancer. Methods: For hybridization to the array, we prepared RNA from MCF-7 human breast ceh tumors, isolated from our athymic nude mouse xenograft model of acquired tamoxifen resistance during estrogen-stimulated, tamoxifen-sensitive, and tamoxifen-resistant growth. Principal components analysis was used to identify genes with altered expression. Results and Conclusions: Principal components analysis yielded three principal components that are interpreted as 1) the average level of gene expression, 2) the difference between estrogen-stimulated gene expression and the average of tamoxifen-sensitive and tamoxifen-resistant gene expression, and 3) the difference between tamoxifen-sensitive and tamoxifen-resistant gene expression. A bivariate (second and third principal components) 99% prediction region was used to identify outlier genes that exhibit altered expression. Two representative outlier genes, erk-2 and HSF-1 (heat shock transcription factor-1), were chosen for confirmatory study, and their predicted relative expression levels were confirmed in western blot analysis, suggesting that semiquantitative estimates are possible with array technology. Implications: Principal components analysis provides a useful and practical method to analyze gene expression data from a cDNA array, The method can identify broad patterns of expression alteration and, based on a small simulation study, will likely provide reasonable power to detect moderate-sized alterations in clinically relevant genes.