Paley Suzanne, Parker Karen, Spaulding Aaron, Tomb Jean-Francois, O'Maille Paul, Karp Peter D
Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA.
Chrysopylae, Los Altos, CA 94024, USA.
Nucleic Acids Res. 2017 Dec 1;45(21):12113-12124. doi: 10.1093/nar/gkx910.
The Omics Dashboard is a software tool for interactive exploration and analysis of gene-expression datasets. The Omics Dashboard is organized as a hierarchy of cellular systems. At the highest level of the hierarchy the Dashboard contains graphical panels depicting systems such as biosynthesis, energy metabolism, regulation and central dogma. Each of those panels contains a series of X-Y plots depicting expression levels of subsystems of that panel, e.g. subsystems within the central dogma panel include transcription, translation and protein maturation and folding. The Dashboard presents a visual read-out of the expression status of cellular systems to facilitate a rapid top-down user survey of how all cellular systems are responding to a given stimulus, and to enable the user to quickly view the responses of genes within specific systems of interest. Although the Dashboard is complementary to traditional statistical methods for analysis of gene-expression data, we show how it can detect changes in gene expression that statistical techniques may overlook. We present the capabilities of the Dashboard using two case studies: the analysis of lipid production for the marine alga Thalassiosira pseudonana, and an investigation of a shift from anaerobic to aerobic growth for the bacterium Escherichia coli.
组学仪表盘是一种用于交互式探索和分析基因表达数据集的软件工具。组学仪表盘被组织成细胞系统的层次结构。在层次结构的最高级别，仪表盘包含描绘生物合成、能量代谢、调控和中心法则等系统的图形面板。每个面板都包含一系列X-Y图，描绘该面板子系统的表达水平，例如中心法则面板内的子系统包括转录、翻译以及蛋白质成熟和折叠。仪表盘呈现细胞系统表达状态的可视化读数，以方便用户从整体到局部快速了解所有细胞系统如何对给定刺激做出反应，并使用户能够快速查看特定感兴趣系统内基因的反应。虽然仪表盘是对分析基因表达数据的传统统计方法的补充，但我们展示了它如何能够检测到统计技术可能忽略的基因表达变化。我们通过两个案例研究展示了仪表盘的功能：对海洋藻类假微型海链藻脂质产生的分析，以及对大肠杆菌从厌氧生长到需氧生长转变的研究。
