Division of Applied Life Science (Brain Korea 21-World Class University Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea.
Mol Cells. 2012 Sep;34(3):295-304. doi: 10.1007/s10059-012-0117-z. Epub 2012 Sep 7.
Independent Component Analysis (ICA) has been introduced as one of the useful tools for gene-functional discovery in animals. However, this approach has been poorly utilized in the plant sciences. In the present study, we have exploited ICA combined with pathway enrichment analysis to address the statistical challenges associated with genome-wide analysis in plant system. To generate an Arabidopsis metabolic platform, we collected 4,373 Affy-metrix ATH1 microarray datasets. Out of the 3,232 metabolic genes and transcription factors, 99.47% of these genes were identified in at least one component, indicating the coverage of most of the metabolic pathways by the components. During the metabolic pathway enrichment analysis, we found components that indicate an independent regulation between the isoprenoid biosynthesis pathways. We also utilized this analysis tool to investigate some transcription factors involved in secondary cell wall biogenesis. This approach has identified remarkably more transcription factors compared to previously reported analysis tools. A website providing user-friendly searching and downloading of the entire dataset analyzed by ICA is available at http://kimjy.gnu.ac.kr/ICA.files/slide0002.htm . ICA combined with pathway enrichment analysis might provide a powerful approach for the extraction of the components responsible for a biological process of interest in plant systems.
独立成分分析 (ICA) 已被引入动物基因功能发现的有用工具之一。然而，这种方法在植物科学中应用较少。在本研究中，我们利用 ICA 结合通路富集分析来解决与植物系统全基因组分析相关的统计挑战。为了生成拟南芥代谢平台，我们收集了 4373 个 Affy-metrix ATH1 微阵列数据集。在 3232 个代谢基因和转录因子中，至少有一个组件中鉴定出了 99.47%的基因，表明组件涵盖了大多数代谢途径。在代谢通路富集分析中，我们发现了一些组件，表明类异戊二烯生物合成途径之间存在独立调控。我们还利用此分析工具研究了一些参与次生细胞壁生物发生的转录因子。与之前报道的分析工具相比，这种方法鉴定出了更多的转录因子。一个提供用户友好的搜索和下载 ICA 分析的整个数据集的网站可在 http://kimjy.gnu.ac.kr/ICA.files/slide0002.htm 获得。ICA 结合通路富集分析可能为提取植物系统中感兴趣的生物过程的负责成分提供一种强大的方法。
