Pathway processor: A tool for integrating whole-genome expression results into metabolic networks
Pathway processor: A tool for integrating whole-genome expression results into metabolic networks
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DOI：
10.1101/gr.226602
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发表时间：
2002-07-01
期刊：
影响因子：
7
通讯作者：
Cavalieri, D
中科院分区：
文献类型：
--
作者：
Grosu, P;Townsend, JP;Cavalieri, D
我们已经开发了一种新工具来可视化代谢途径的表达数据，并评估哪些代谢途径受到全基因组表达实验的转录变化影响最大的代谢途径。使用Fisher精确检验，该方法根据途径中的许多或更多基因在给定的实验中仅偶然地将显着改变途径中的许多或更多基因的可能性。该方法已在Diauxic Shift实验中得到验证，并再现了碳源对酵母代谢的众所周知的影响。该分析是用途径分析仪（Pathway Analyzer）（途径处理器的工具之一）实施的，这是一种新的统计软件包，用于分析全基因组表达数据。可以比较多个实验的结果，从而将整个单个基因的分析降低到有限的感兴趣途径。使用Opendix（开源可视化软件包）可视化途径，并且可以使用该软件包的第二个程序表达式Mapper详细检查途径中的基因之间的关系。该程序具有图形输出，显示在分配开放式阅读框的生化途径的代谢图表上表达式差异。
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 OpenDix, 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.