Paley Suzanne, Billington Richard, Herson James, Krummenacker Markus, Karp Peter D
Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA.
Robotics Group, SRI International, Menlo Park, CA 94025, USA.
Metabolites. 2021 Jan 22;11(2):64. doi: 10.3390/metabo11020064.
Metabolomics, synthetic biology, and microbiome research demand information about organism-scale metabolic networks. The convergence of genome sequencing and computational inference of metabolic networks has enabled great progress toward satisfying that demand by generating metabolic reconstructions from the genomes of thousands of sequenced organisms. Visualization of whole metabolic networks is critical for aiding researchers in understanding, analyzing, and exploiting those reconstructions. We have developed bioinformatics software tools that automatically generate a full metabolic-network diagram for an organism, and that enable searching and analyses of the network. The software generates metabolic-network diagrams for unicellular organisms, for multi-cellular organisms, and for pan-genomes and organism communities. Search tools enable users to find genes, metabolites, enzymes, reactions, and pathways within a diagram. The diagrams are zoomable to enable researchers to study local neighborhoods in detail and to see the big picture. The diagrams also serve as tools for comparison of metabolic networks and for interpreting high-throughput datasets, including transcriptomics, metabolomics, and reaction fluxes computed by metabolic models. These data can be overlaid on the metabolic charts to produce animated zoomable displays of metabolic flux and metabolite abundance. The BioCyc.org website contains whole-network diagrams for more than 18,000 sequenced organisms. The ready availability of organism-specific metabolic network diagrams and associated tools for almost any sequenced organism are useful for researchers working to better understand the metabolism of their organism and to interpret high-throughput datasets in a metabolic context.
代谢组学、合成生物学和微生物组研究需要有关生物体规模代谢网络的信息。基因组测序与代谢网络的计算推断相结合，通过从数千个已测序生物体的基因组中生成代谢重建，在满足这一需求方面取得了巨大进展。整个代谢网络的可视化对于帮助研究人员理解、分析和利用这些重建至关重要。我们开发了生物信息学软件工具，可自动为生物体生成完整的代谢网络图，并能对该网络进行搜索和分析。该软件可为单细胞生物、多细胞生物、泛基因组和生物体群落生成代谢网络图。搜索工具可让用户在图中查找基因、代谢物、酶、反应和途径。这些图可缩放，使研究人员能够详细研究局部区域并了解整体情况。这些图还可作为比较代谢网络和解释高通量数据集的工具，包括转录组学、代谢组学以及由代谢模型计算得出的反应通量。这些数据可叠加在代谢图上，以生成代谢通量和代谢物丰度的动态可缩放显示。BioCyc.org网站包含超过18000个已测序生物体的全网络图。几乎为任何已测序生物体提供特定生物体的代谢网络图及相关工具，对致力于更好地理解其生物体代谢并在代谢背景下解释高通量数据集的研究人员很有用。
