Robust estimation of protein expression ratios with lysate microarray technology
Robust estimation of protein expression ratios with lysate microarray technology
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DOI：
10.1093/bioinformatics/bti258
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发表时间：
2005-05-01
期刊：
影响因子：
5.8
通讯作者：
Zhang, W
中科院分区：
文献类型：
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作者：
Mircean, C;Shmulevich, I;Zhang, W
动机：蛋白质裂解物微阵列是一种新兴的蛋白质组学技术，用于同时测量大量生物样品中的蛋白质表达水平。准确定量的挑战是与常用的显色信号检测系统相关的相对窄的动态范围。为了便于准确测量相对表达水平，将每个样品连续稀释，并将每个稀释版本一式三份点样在硝化纤维素包被的载玻片上。因此，每个样品在检测系统的不同动态范围内产生多个测量值。本研究的目的是开发合适的算法，产生准确的表示在不同的样品中的相对表达水平从多个datapoints.Results：我们评估了两种算法估计相对蛋白质表达在不同的样品上的裂解物微阵列通过交叉验证程序。为了这个目的，以及质量控制，我们设计了一个1440点裂解物微阵列含有80个相同的样品纯化牛血清白蛋白，打印一式三份，6个2倍稀释。我们的分析表明，基于鲁棒最小二乘估计的算法提供了最准确的定量的蛋白质裂解物微阵列数据。我们还通过在另一个裂解物微阵列上估计两种药物治疗及其组合后p53（+/+）或p53（-/-）HCT 116结肠癌细胞中p53和p21的相对表达水平来证明我们的方法。
Motivation: The protein lysate microarray is a developing proteomic technology for measuring protein expression levels in a large number of biological samples simultaneously. A challenge for accurate quantification is the relatively narrow dynamic range associated with the commonly used chromogenic signal detection system. To facilitate accurate measurement of the relative expression levels, each sample is serially diluted and each diluted version is spotted on a nitrocellulose-coated slide in triplicate. Thus, each sample yields multiple measurements in different dynamic ranges of the detection system. This study aims to develop suitable algorithms that yield accurate representations of the relative expression levels in different samples from multiple data points.Results: We evaluated two algorithms for estimating relative protein expression in different samples on the lysate microarray by means of a cross-validation procedure. For this purpose as well as for quality control we designed a 1440-spot lysate microarray containing 80 identical samples of purified bovine serum albumin, printed in triplicate with six 2-fold dilutions. Our analysis showed that the algorithm based on a robust least squares estimator provided the most accurate quantification of the protein lysate microarray data. We also demonstrated our methods by estimating relative expression levels of p53 and p21 in either p53(+/+) or p53(-/-) HCT116 colon cancer cells after two drug treatments and their combinations on another lysate microarray.