Symons Stephan, Zipplies Christian, Battke Florian, Nieselt Kay
Center for Bioinformatics Tübingen, University of Tübingen, Sand 14, 72076 Tübingen, Germany. ed.negnibeut-inu.kitamrofni@nullsnomys
J Integr Bioinform. 2010 Mar 25;7(3):458. doi: 10.2390/biecoll-jib-2010-115.
Visualization is pivotal for gaining insight in systems biology data. As the size and complexity of datasets and supplemental information increases, an efficient, integrated framework for general and specialized views is necessary. MAYDAY is an application for analysis and visualization of general 'omics' data. It follows a trifold approach for data visualization, consisting of flexible data preprocessing, highly customizable data perspective plots for general purpose visualization and systems based plots. Here, we introduce two new systems biology visualization tools for MAYDAY. Efficiently implemented genomic viewers allow the display of variables associated with genomic locations. Multiple variables can be viewed using our new track-based ChromeTracks tool. A functional perspective is provided by visualizing metabolic pathways either in KEGG or BioPax format. Multiple options of displaying pathway components are available, including Systems Biology Graphical Notation (SBGN) glyphs. Furthermore, pathways can be viewed together with gene expression data either as heatmaps or profiles. We apply our tools to two 'omics' datasets of Pseudomonas aeruginosa. The general analysis and visualization tools of MAYDAY as well as our ChromeTracks viewer are applied to a transcriptome dataset. We furthermore integrate this dataset with a metabolome dataset and compare the activity of amino acid degradation pathways between these two datasets, by visually enhancing the pathway diagrams produced by MAYDAY.
可视化对于洞察系统生物学数据至关重要。随着数据集及补充信息的规模和复杂性不断增加，需要一个高效的、集成的框架来实现通用视图和特定视图。MAYDAY是一款用于分析和可视化通用“组学”数据的应用程序。它采用了一种三重数据可视化方法，包括灵活的数据预处理、用于通用可视化的高度可定制的数据透视图以及基于系统的图。在此，我们为MAYDAY引入了两种新的系统生物学可视化工具。高效实现的基因组查看器能够显示与基因组位置相关的变量。使用我们新的基于轨道的ChromeTracks工具可以查看多个变量。通过以KEGG或BioPax格式可视化代谢途径，提供了一种功能视角。显示途径成分有多种选项，包括系统生物学图形符号（SBGN）图形。此外，途径可以与基因表达数据一起以热图或剖面图的形式查看。我们将我们的工具应用于铜绿假单胞菌的两个“组学”数据集。MAYDAY的通用分析和可视化工具以及我们的ChromeTracks查看器应用于一个转录组数据集。我们还将这个数据集与一个代谢组数据集整合，并通过直观增强MAYDAY生成的途径图，比较这两个数据集之间氨基酸降解途径的活性。
