Grosu Paul, Townsend Jeffrey P, Hartl Daniel L, Cavalieri Duccio
Bauer Center for Genomics Research, Harvard University, Cambridge, Massachusetts 02138, USA.
Genome Res. 2002 Jul;12(7):1121-6. doi: 10.1101/gr.226602.
We have developed a new tool to visualize expression data on metabolic pathways and to evaluate which metabolic pathways are most affected by transcriptional changes in whole-genome expression experiments. Using the Fisher Exact Test, the method scores biochemical pathways according to the probability that as many or more genes in a pathway would be significantly altered in a given experiment by chance alone. This method has been validated on diauxic shift experiments and reproduces well known effects of carbon source on yeast metabolism. The analysis is implemented with Pathway Analyzer, one of the tools of Pathway Processor, a new statistical package for the analysis of whole-genome expression data. Results from multiple experiments can be compared, reducing the analysis from the full set of individual genes to a limited number of pathways of interest. The pathways are visualized with OpenDX, an open-source visualization software package, and the relationship between genes in the pathways can be examined in detail using Expression Mapper, the second program of the package. This program features a graphical output displaying differences in expression on metabolic charts of the biochemical pathways to which the open reading frames are assigned.
我们开发了一种新工具，用于可视化代谢途径上的表达数据，并评估在全基因组表达实验中哪些代谢途径受转录变化影响最大。该方法使用Fisher精确检验，根据一个途径中在给定实验中仅因偶然因素就有同样多或更多基因发生显著改变的概率，对生化途径进行评分。此方法已在二次生长转换实验中得到验证，能够重现碳源对酵母代谢的已知影响。该分析通过Pathway Analyzer来实现，它是Pathway Processor的工具之一，Pathway Processor是一个用于分析全基因组表达数据的新统计软件包。可以比较多个实验的结果，将对全套单个基因的分析简化为有限数量的感兴趣途径。这些途径通过开源可视化软件包OpenDX进行可视化，并且可以使用该软件包的第二个程序Expression Mapper详细检查途径中基因之间的关系。该程序的特点是在分配了开放阅读框的生化途径的代谢图上以图形输出显示表达差异。
