Li Feng, Seillier-Moiseiwitsch Françoise
Department of Mathematics and Statistics, University of Maryland, Baltimore County, Baltimore, Maryland, USA.
Methods Enzymol. 2011;487:595-609. doi: 10.1016/B978-0-12-381270-4.00021-4.
Two-dimensional polyacrylomide gel electrophoresis remains a popular and powerful tool for identifying proteins that are differentially expressed across treatment conditions. Due to the overwhelming number of proteins and the tremendous variation shown in gel images, the differential analysis of 2D gel images is challenging. While commercial software packages are available for such analysis, they require considerable human intervention for spot detection and matching. Moreover, the quantitative comparison across groups of gels is based on simple classical tests that often do not fully account for the experimental design. We developed software with a graphical user interface, RegStatGel, which implements a novel statistical algorithm for identifying differentially expressed proteins. Unlike current commercial software packages, it is free, open-source, easy to use and almost fully automated. It also provides more advanced statistical tools. More importantly, by using a master watershed map, RegStatGel bypasses the spot-matching procedure, which is a time-consuming bottleneck in gel image analysis. The software is freely available for academic use and has been tested in Matlab 7.01 under Windows XP. Detailed instructions on how to use RegStatGel to analyze 2D gel images are provided.
二维聚丙烯酰胺凝胶电泳仍然是一种常用且强大的工具，用于鉴定在不同处理条件下差异表达的蛋白质。由于蛋白质数量众多且凝胶图像显示出巨大差异，二维凝胶图像的差异分析具有挑战性。虽然有商业软件包可用于此类分析，但它们在斑点检测和匹配方面需要大量人工干预。此外，跨凝胶组的定量比较基于简单的经典测试，这些测试往往不能充分考虑实验设计。我们开发了一款带有图形用户界面的软件RegStatGel，它实现了一种用于鉴定差异表达蛋白质的新颖统计算法。与当前的商业软件包不同，它是免费的、开源的、易于使用且几乎完全自动化。它还提供了更先进的统计工具。更重要的是，通过使用主分水岭图，RegStatGel绕过了斑点匹配过程，而这是凝胶图像分析中耗时的瓶颈。该软件可供学术免费使用，并已在Windows XP系统下的Matlab 7.01中进行了测试。文中提供了关于如何使用RegStatGel分析二维凝胶图像的详细说明。
