EcoCyc

[…] e de-facto standard in species-specific database curation, and Pathway Tools generated and manually curated PGDBs have been created across the domains of life, including bacteria [Escherichia coli in EcoCyc ()], fungi (Saccharomyces cerevisiae in YeastCyc http://yeast.biocyc.org/), mammals [Bos taurus in CattleCyc ()] and plants such as Arabidopsis thaliana in AraCyc (, ), Medicago truncatula in M […]

[…] ds) using exact mass and predicted retention time based on the Kyoto Encyclopedia of Genes and Genomes (KEGG), MetaCyc, and LIPIDMAPS databases, using preference to bacterial metabolites annotated in EcoCyc. Raw peak intensity was used to quantify each metabolite. The free online tool MetaboAnalyst 3.0 was used for the statistical analysis. Briefly, putative metabolites with median RSD ≤ 0.2 (20%) […]

[…] ons of GenDev based on three techniques, A, B and C; using two solvers, SCIP and CPLEX; and using two methods for MILP formulation, called Big M and indicators. We randomly removed reactions from the EcoCyc-20.0-GEM metabolic model, ran each of the 13 gap-filler variations on the resulting reaction network, and assessed how closely the resulting set of reactions matched the removed set of reaction […]

[…] the 23 putative CRP-binding sites have high probability to be CRP-binding sites according to the consensus sequence criterion, we further proved the 23 sites as CRP-binding sites by referring to the EcoCyc database (see Supporting Information). The 23 predicted CRP-regulated interactions are given in Figure , which were validated by qPCR experiments. […]

[…] vely, the Chemical Translation Service and UniChem provide a simple web application that can interconvert metabolite IDs across different databases. Organism-specific GSMs or knowledge-bases (e.g., EcoCyc , AraCyc , and HumanCyc ) are often constructed or extracted from the larger databases, to ensure the design or identification of alternative pathways within an organism's native network. While […]

[…] y rate in multiple testing). Genes and their fold-changes can be found in File S1.Gene ontology (GO) analysis was carried out using the R package topGO (). E. coli gene annotations were obtained from Ecocyc ( p. 2014) and GO terms were obtained from the GO Consortium (). In topGO, the Fisher test was used to assess significance of enriched gene sets and terms with P values <0.01 were considered si […]