Visualizing metabolic activity on a genome-wide scale
Visualizing metabolic activity on a genome-wide scale
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DOI：
10.1093/bioinformatics/18.6.813
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发表时间：
2002-06-01
期刊：
影响因子：
5.8
通讯作者：
van Kampen, AHC
中科院分区：
文献类型：
--
作者：
Luyf, ACM;de Gast, J;van Kampen, AHC
动机：为了加强对代谢背景下基因表达数据的探索，需要一种应用程序来集成这些数据，并在（全基因组）代谢图谱中表示这些数据。该代谢图的布局必须高度灵活，以便能够发现生物现象。此外，它必须允许同时表示有关基因和酶的附加信息。由于现有图谱的布局和属性不能满足我们的要求，我们开发了一种在代谢图表中表示基因表达数据的新方法。结果：ViMAc 生成用户指定的（全基因组）代谢图谱来探索基因表达数据。为了增强对这些图谱的解释，还包括了亚细胞定位等信息。 ViMAc 可用于分析通过 DNA 微阵列或 SAGE 获得的人类或酵母表达数据。我们介绍了我们的代谢图谱方法，并演示了如何应用它来探索酵母的 DNA 微阵列数据。
Motivation: To enhance the exploration of gene expression data in a metabolic context, one requires an application that allows the integration of this data and which represents this data in a (genome-wide) metabolic map. The layout of this metabolic map must be highly flexible to enable discoveries of biological phenomena. Moreover, it must allow the simultaneous representation of additional information about genes and enzymes. Since the layout and properties of existing maps did not fulfill our requirements, we developed a new way of representing gene expression data in metabolic charts.Results: ViMAc generates user-specified (genome-wide) metabolic maps to explore gene expression data. To enhance the interpretation of these maps information such as sub-cellular localization is included. ViMAc can be used to analyse human or yeast expression data obtained with DNA microarrays or SAGE. We introduce our metabolic map method and demonstrate how it can be applied to explore DNA microarray data for yeast.