Paley Suzanne, Caspi Ron, O'Maille Paul, Karp Peter D
Bioinformatics Research Group, SRI International, Menlo Park, CA, United States.
Biosciences Division, SRI International, Menlo Park, CA, United States.
Front Microbiol. 2024 Jul 31;15:1447632. doi: 10.3389/fmicb.2024.1447632. eCollection 2024.
The Comparative Genome Dashboard is a web-based software tool for interactive exploration of the similarities and differences in gene functions between organisms. It provides a high-level graphical survey of cellular functions, and enables the user to drill down to examine subsystems of interest in greater detail. At its highest level the Comparative Dashboard contains panels for cellular systems such as biosynthesis, energy metabolism, transport, and response to stimulus. Each panel contains a set of bar graphs that plot the numbers of compounds or gene products for each organism across a set of subsystems of that panel. Users can interactively drill down to focus on subsystems of interest and see grids of compounds produced or consumed by each organism, specific GO term assignments, pathway diagrams, and links to more detailed comparison pages. For example, the dashboard enables users to compare the cofactors that a set of organisms can synthesize, the metal ions that they are able to transport, their DNA damage repair capabilities, their biofilm-formation genes, and their viral response proteins. The dashboard enables users to quickly perform comprehensive comparisons at varying levels of detail.
比较基因组仪表板是一个基于网络的软件工具，用于交互式探索不同生物体之间基因功能的异同。它提供了细胞功能的高级图形化概览，并能让用户深入探究感兴趣的子系统的更多细节。在最高层级，比较仪表板包含用于细胞系统的面板，如生物合成、能量代谢、运输以及对刺激的反应。每个面板都包含一组柱状图，展示了每个生物体在该面板的一组子系统中化合物或基因产物的数量。用户可以交互式地深入探究，聚焦于感兴趣的子系统，并查看每个生物体产生或消耗的化合物网格、特定的基因本体（GO）术语分配、通路图以及指向更详细比较页面的链接。例如，仪表板能让用户比较一组生物体能够合成的辅因子、它们能够运输的金属离子、它们的DNA损伤修复能力、它们的生物膜形成基因以及它们的病毒反应蛋白。该仪表板能让用户在不同详细程度上快速进行全面比较。
