Karp Peter D, Paley Suzanne, Caspi Ron, Kothari Anamika, Krummenacker Markus, Midford Peter E, Moore Lisa R, Subhraveti Pallavi, Gama-Castro Socorro, Tierrafria Victor H, Lara Paloma, Muñiz-Rascado Luis, Bonavides-Martinez César, Santos-Zavaleta Alberto, Mackie Amanda, Sun Gwanggyu, Ahn-Horst Travis A, Choi Heejo, Covert Markus W, Collado-Vides Julio, Paulsen Ian
Bioinformatics Research Group, SRI International, Menlo Park, California, USA.
Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
EcoSal Plus. 2023 Dec 12;11(1):eesp00022023. doi: 10.1128/ecosalplus.esp-0002-2023. Epub 2023 May 11.
EcoCyc is a bioinformatics database available online at EcoCyc.org that describes the genome and the biochemical machinery of K-12 MG1655. The long-term goal of the project is to describe the complete molecular catalog of the cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of . EcoCyc is an electronic reference source for biologists and for biologists who work with related microorganisms. The database includes information pages on each gene product, metabolite, reaction, operon, and metabolic pathway. The database also includes information on the regulation of gene expression, gene essentiality, and nutrient conditions that do or do not support the growth of . The website and downloadable software contain tools for the analysis of high-throughput data sets. In addition, a steady-state metabolic flux model is generated from each new version of EcoCyc and can be executed online. The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. Data generated from a whole-cell model that is parameterized from the latest data on EcoCyc are also available. This review outlines the data content of EcoCyc and of the procedures by which this content is generated.
EcoCyc是一个可在EcoCyc.org在线获取的生物信息学数据库，它描述了K-12 MG1655的基因组和生化机制。该项目的长期目标是描述细胞的完整分子目录及其每个分子部分的功能，以促进对系统层面的理解。EcoCyc是生物学家以及研究相关微生物的生物学家的电子参考来源。该数据库包括关于每个基因产物、代谢物、反应、操纵子和代谢途径的信息页面。该数据库还包括关于基因表达调控、基因必需性以及支持或不支持其生长的营养条件的信息。该网站和可下载软件包含用于分析高通量数据集的工具。此外，从EcoCyc的每个新版本生成一个稳态代谢通量模型，并可在线执行。该模型可以预测不同基因敲除和营养条件下的代谢通量率、营养吸收速率和生长速率。还提供了根据EcoCyc的最新数据参数化的全细胞模型生成的数据。本综述概述了EcoCyc的数据内容以及生成此内容的程序。
