Microarrays are at the center of a revolution in biotechnology, allowing researchers to simultaneously monitor the expression of tens of thousands genes, having been widely used in medical research. The main chal⁃lenge is to extract useful information from such gene expression profile and then implement biological interpreta⁃tion. Pathway analysis has become the first choice for gaining insight into the underlying biology of differentially expressed genes and proteins, as it reduces complexity and has increased explanatory power. We discussed the evo⁃lution of knowledge base-driven pathway analysis over its first decade, distinctly divided into three generations. We also discussed the limitations that are specific to each generation, and how they are addressed by successive generations of methods.% 微阵列技术是生物技术变革的核心，允许研究者同时监测成千上万个基的表达水平，已广泛应用医学研究。如何挖掘海量基表达信息中的有用信息并进行生物学专业解释，是基表达谱数据分析领所面临的一个重要挑战。生物信号通路研究已成为基芯片中不同表型差异表达研究的主要方法，其是以整个信号通路作为一个整体作为研究对象，此得出的研究结果更加科学和准确。在本文中我们简要描述了近10年来信号通路基集富集分析方法的发展情况，将其分为三个阶段，对每个阶段方法的基础和特点做了一些简单的总结和阐述。
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