Pathway Tools Visualization of Organism-Scale Metabolic Networks.
Pathway Tools Visualization of Organism-Scale Metabolic Networks.
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DOI：
10.3390/metabo11020064
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发表时间：
2021-01-22
期刊：
影响因子：
4.1
通讯作者：
Karp PD
中科院分区：
文献类型：
--
作者：
Paley S;Billington R;Herson J;Krummenacker M;Karp PD
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。基因组测序和代谢网络的计算推理的融合，通过从数千个已测序生物的基因组中产生代谢重建，使满足这一需求的工作取得了巨大进展。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是至关重要的。我们已经开发了生物信息学软件工具，可以自动生成生物体的完整代谢网络图，并能够对网络进行搜索和分析。该软件为单细胞生物体、多细胞生物体、泛基因组和生物群落生成代谢网络图。搜索工具使用户能够在图表中找到基因、代谢物、酶、反应和途径。这些图表可以缩放，使研究人员能够详细研究当地社区，并看到整体情况。这些图表还用作比较代谢网络和解释高通量数据集的工具，包括转录组学、代谢组学和代谢模型计算的反应通量。这些数据可以叠加在代谢图上，以生成代谢流量和代谢物丰度的动态可缩放显示。BioCyc.org网站包含超过18,000种已测序生物的全网络图。几乎所有已测序生物体的特定生物体代谢网络图和相关工具的现成可用，对于致力于更好地了解其生物体的新陈代谢并在新陈代谢背景下解释高通量数据集的研究人员是有用的。
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.
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影响因子：
4.3
作者：
King ZA;Dräger A;Ebrahim A;Sonnenschein N;Lewis NE;Palsson BO
通讯作者：
Palsson BO
影响因子：
17.3
作者：
Karp, PP;Krummenacker, M;Wagg, J
通讯作者：
Wagg, J
DOI：
10.1007/978-1-61779-361-5_11
发表时间：
2012-01-01
期刊：
BACTERIAL MOLECULAR NETWORKS: METHODS AND PROTOCOLS
影响因子：
--
作者：
Latendresse, Mario;Paley, Suzanne;Karp, Peter D.
通讯作者：
Karp, Peter D.
影响因子：
5.8
作者：
Latendresse, Mario;Krummenacker, Markus;Karp, Peter D.
通讯作者：
Karp, Peter D.
影响因子：
14.9
作者：
Paley, Suzanne M.;Karp, Peter D.
通讯作者：
Karp, Peter D.