Normalization and expression changes in predefined sets of proteins using 2D gel electrophoresis: a proteomic study of L-DOPA induced dyskinesia in an animal model of Parkinson's disease using DIGE.
Normalization and expression changes in predefined sets of proteins using 2D gel electrophoresis: a proteomic study of L-DOPA induced dyskinesia in an animal model of Parkinson's disease using DIGE.
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使用2D凝胶电泳的预定蛋白组中的归一化和表达变化：L-DOPA诱导的蛋白质组学研究在帕金森氏病动物模型中使用DIGE进行了蛋白质组学研究。
DOI：
10.1186/1471-2105-7-475
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发表时间：
2006-10-26
影响因子：
3
通讯作者：
Lonnstedt, Ingrid
中科院分区：
文献类型：
--
作者：
Kultima, Kim;Scholz, Birger;Alm, Henrik;Skold, Karl;Svensson, Marcus;Crossman, Alan R.;Bezard, Erwan;Andren, Per E.;Lonnstedt, Ingrid
二维差异凝胶电泳 (2D-DIGE) 是测量样品或条件之间蛋白质表达差异的强大工具。然而，为了消除凝胶内和凝胶之间的系统变异性，必须对数据进行标准化。在这项研究中，我们检查了四种现有的标准化方法和四种新颖的标准化方法消除 2D-DIGE 生成的数据中的系统偏差的能力。我们还提出了对现有方法的修改，其中统计框架确定一组蛋白质是否显示出与预定义的感兴趣表型的关联。该方法应用于我们从帕金森病猴子模型（食蟹猴）生成的数据。使用 2D-DIGE，我们分析了 6 只对照猴子和 21 只 MPTP 处理的猴子纹状体的蛋白质含量，无论是否从头或长期施用 L-DOPA。本研究中检查的所有凝胶的数据都存在强度和空间偏差。评估的八种归一化方法中只有两种（“2D loess+scale”和“SC-2D+分位数”）成功消除了强度和空间偏差。在“SC-2D+分位数”中，我们扩展了常用的黄土标准化方法来对抗双通道微阵列系统中的染料偏差，以适应具有三个或更多通道的系统。此外，通过使用所提出的方法，预定义蛋白质组中的差异表达（DEPPS），鉴定了与帕金森病动物纹状体中左旋多巴的启动效应相关的几组蛋白质。其中三组是参与能量代谢的蛋白质，一组涉及微管细胞骨架一部分的蛋白质。根据实验设计，对不同方法进行比较，得出一系列用于数据标准化和分析的方法学建议。由于 2D-DIGE 数据的性质，我们建议在显着性检验中获得的 p 值仅用作排名。单个蛋白质本身可能很有趣，但通过研究蛋白质组，对结果的解释可能会更准确且具有生物学信息。
Two-Dimensional Difference In Gel Electrophoresis (2D-DIGE) is a powerful tool for measuring differences in protein expression between samples or conditions. However, to remove systematic variability within and between gels the data has to be normalized. In this study we examined the ability of four existing and four novel normalization methods to remove systematic bias in data produced with 2D-DIGE. We also propose a modification of an existing method where the statistical framework determines whether a set of proteins shows an association with the predefined phenotypes of interest. This method was applied to our data generated from a monkey model (Macaca fascicularis) of Parkinson's disease. Using 2D-DIGE we analysed the protein content of the striatum from 6 control and 21 MPTP-treated monkeys, with or without de novo or long-term L-DOPA administration. There was an intensity and spatial bias in the data of all the gels examined in this study. Only two of the eight normalization methods evaluated ('2D loess+scale' and 'SC-2D+quantile') successfully removed both the intensity and spatial bias. In 'SC-2D+quantile' we extended the commonly used loess normalization method against dye bias in two-channel microarray systems to suit systems with three or more channels. Further, by using the proposed method, Differential Expression in Predefined Proteins Sets (DEPPS), several sets of proteins associated with the priming effects of L-DOPA in the striatum in parkinsonian animals were identified. Three of these sets are proteins involved in energy metabolism and one set involved proteins which are part of the microtubule cytoskeleton. Comparison of the different methods leads to a series of methodological recommendations for the normalization and the analysis of data, depending on the experimental design. Due to the nature of 2D-DIGE data we recommend that the p-values obtained in significance tests should be used as rankings only. Individual proteins may be interesting as such, but by studying sets of proteins the interpretation of the results are probably more accurate and biologically informative.
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影响因子：
6.1
作者：
Bezard, E;Gross, CE;Gurevich, EV
通讯作者：
Gurevich, EV
影响因子：
3.4
作者：
Guigoni, C;Dovero, S;Bezard, E
通讯作者：
Bezard, E
影响因子：
82.9
作者：
Bézard, E;Ferry, S;Sokoloff, P
通讯作者：
Sokoloff, P
影响因子：
3.5
作者：
Cappelletti, G;Surrey, T;Maci, R
通讯作者：
Maci, R
影响因子：
5.8
作者：
Fodor, IK;Nelson, DO;McCutchen-Maloney, SL
通讯作者：
McCutchen-Maloney, SL