ECOCYC DATABASE PDF

In bioinformatics EcoCyc is a biological database for the bacterium Escherichia coli K The EcoCyc project performs literature-based curation of the E. coli. PDF | EcoCyc is a bioinformatics database available at that describes the genome and the biochemical machinery of Escherichia. EcoCyc is a scientific database for the bacterium Escherichia coli K MG The EcoCyc project performs literature-based curation of the.

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EcoCyc is a bioinformatics database available at EcoCyc. The long-term goal of the project is to describe the complete molecular catalog of the E. EcoCyc is an electronic reference source for E. The database includes information pages on each E. The database also includes information on E. The web site and downloadable software contain tools for analysis of high-throughput datasets. In addition, a steady-state metabolic flux model is generated from each new version of EcoCyc.

The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. This chapter provides a detailed description of the data content of EcoCyc, and of the procedures by which this content is generated.

EcoCyc 1 is a bioinformatics database that describes the genome and the biochemical machinery of E.

The EcoCyc Model Organism Database for Escherichia coli [SRI Proposal ECU ] – Peter Karp

In addition to the database, a steady-state metabolic flux model is databae, generated from each new version of EcoCyc. EcoCyc is designed for several different modes of interactive use via both the EcoCyc. Users of EcoCyc fall into several different groups.

Experimental biologists use EcoCyc as an encyclopedic reference on genes, pathways, and regulation, and they use its omics-data analysis tools to analyze gene-expression and metabolomics data. Examples of papers citing EcoCyc in the analysis of functional genomics data include: Because the EcoCyc data are structured ecofyc a sophisticated ontology that is amenable to computational analyses, EcoCyc enables scientists to ask computational questions spanning the ecoccyc genome of E. Past work includes use of EcoCyc to develop methods for studying path lengths within metabolic networks [ 789 ]; in studies relating protein structure to the metabolic network [ 1011 ]; and in analysis of the E.

The development of many new bioinformatics methods requires high-quality, gold-standard datasets for the training and validation of those methods.

EcoCyc – Wikipedia

EcoCyc has been used as a gold-standard dataset for the development of genome-context methods for predicting gene function [ 1415 ], operon-prediction methods [ 1617 ], prediction of promoters and transcription start sites [ 1819 ], regulatory network reconstruction [ 20 ], and the prediction of functional and direct protein-protein interactions [ 212223 ]. Metabolic engineers alter microbes to produce biofuels, industrial chemicals, and pharmaceuticals; to de-grade toxic pollutants; and dahabase sequester carbon [ 272829 ].

Metabolic engineers who use E. Metabolic engineering studies using EcoCyc include [ 303132 ]. According to the Thomson Reuters Web of Knowledge citation index, as of Augustthe 23 EcoCyc and RegulonDB papers authored since were cited by 2, publications from — According to Google Analytics, approximatelyvisitors query the EcoCyc website each year, generatingobject page views per month on average in EcoCyc data are available for download in multiple file formats see http: EcoCyc covers a broad array of data types.

Key to understanding the EcoCyc data and its presentation ecofyc the EcoCyc website and Pathway Tools is the notion of a database class, which describes a specific type of data.

For example, the class Genes provides the database definition of a gene, including the attributes e.

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The EcoCyc Database

Each specific gene within EcoCyc is stored in a single database object, or frame, that is an instance of the class Genes. No one-to-one databbase exists between EcoCyc classes and the data pages within the EcoCyc website, because one data page typically integrates information from multiple classes.

For example, the pathway data page integrates information from objects in the classes Pathways, Reactions, Genes, Proteins, and Chemicals. EcoCyc contains the complete genome sequence of E. EcoCyc data on the essentiality of E.

EcoCyc describes wcocyc known monomers and multimeric protein complexes of E. EcoCyc contains extensive annotation of the features of E. EcoCyc contains the most complete description of the regulatory network of any organism. Each molecular regulatory interaction is described as an instance of class Regulation, whose subclasses describe different types of regulation.

EcoCyc describes all known metabolic and signal-transduction pathways of E. It describes each metabolic enzyme of E. EcoCyc integrates data on the growth of E. EcoCyc is linked to other biological databases containing protein and nucleic acid sequence data, bibliographic data, protein structures, and ratabase of different E. Curation is the process of manually refining and updating a bioinformatics database.

The EcoCyc project uses a literature-based curation approach in which database updates are based on evidence in the experimental literature. EcoCyc is largely up to date with respect to its curation activities. As of OctoberEcoCyc encodes information from more than 25, publications. A staff of four full-time curators updates the annotation of the E.

Julio Collado-Vides at the UNAM; therefore, both databases include the same data content on transcriptional regulation of gene expression. The actual data curation occurs within EcoCyc, and the information is periodically propagated to RegulonDB.

Curators collect gene, protein, pathway, and compound names and synonyms. They classify genes and gene products using the Gene Ontology [ 34 ] and MultiFun [ 35 ] ontologies, and they classify pathways within the Pathway Tools pathway ontology.

Protein complex components and the stoichiometry of these subunits are captured; cellular localization of polypeptides and protein complexes is entered, as are experimentally determined protein molecular weights; enzyme activities and any enzyme prosthetic groups, cofactors, activators, or inhibitors are captured. Operon structure and gene regulation information are encoded. Curators author textual summaries with extensive citations. Within the summaries for proteins, RNAs, pathways, and operons, curators capture additional information not otherwise captured in the highly structured database fields of EcoCyc.

For example, curators use the free-text ecicyc sections to describe the overall function of a gene product, the phenotypes caused by mutation, depletion, or overproduction of each gene product; any known genetic interactions; protein domain architecture and structural studies; the similarity to other proteins; or any functional complementation experiments that have been described.

Summaries can also be used to note cases in which ecicyc published reports present contradictory results. In such cases, both viewpoints will be presented with proper attribution. This approach strives to ensure that no information is lost. EcoCyc entries are generally updated when new literature becomes available. Regular PubMed searches are used to generate lists of potentially curatable publications, which are then evaluated and prioritized for curation.

Papers containing newly identified functions of gene products, as well as substantial advances in understanding the functions of known gene products, are given the highest priority for curation.

Because the Pathway Tools software continues to evolve and to enable the addition of new data types, older entries are also being updated in a systematic fashion e. The databaxe numbers are current as of version Genes and gene products in EcoCyc. Protein features are annotations of protein sites and regions such as enzyme active sites, metal ion binding sites, and transmembrane domains.

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A small number of IS elements are included in the count of Genes but are not included in the sub-categories of genes. Gene annotation status in EcoCyc. Genes of known molecular function have experimental evidence for databzse assigned function, whereas genes of predicted ecocyx function have had their function predicted computationally.

Reactions, compounds and pathways in EcoCyc.

Superpathways are connected sets of base metabolic pathways connected via shared substrates. Regulation-related objects and interactions in EcoCyc. As ofEcoCyc incorporates media that have been shown experimentally to support or not support growth of both wildtype and knock-out strains of E. This work has two goals.

EcoCyc Database

First is to assemble a comprehensive encyclopedia of E. The spectrum of environmental conditions supporting the growth of a bacterium is among its most important phenotypic traits. We cannot expect to understand the functions of all genes in an organism unless we understand the full range of environments in which the cell can grow. Second, a comprehensive collection of E.

The larger the set of growth media against which these computational models are validated, the more accurate and comprehensive that the models will be.

EcoCyc captures approximately 20 media that are commonly used by E. EcoCyc also records the results of high-throughput experiments using Biolog Phenotype Microarrays PMswhich ecpcyc cell respiration as a sensitive indicator of microbial growth [ 36 ].

The commercially available PM system for microorganisms provides a comprehensive set of phenotype tests including information on the ability to metabolize carbon C compounds, 95 nitrogen N compounds, 59 phosphorus P compounds, and 35 sulfur S compounds.

EcoCyc currently documents five sets of PM data from the following sources:. The coloring of each box indicates the degree of growth observed under that condition. Three levels of growth are recorded: Click on any growth medium to request a databaase describing its composition, and to see genes that are essential or not essential for growth under that condition.

As ofEcoCyc incorporates several large-scale datasets on gene essentiality in E. Gene essentiality information is useful for. When essentiality data is available for a given gene, the EcoCyc gene page includes a table of the conditions under which that gene has been found to be either essential or not essential for growth.

Clicking on the condition will navigate to a growth-medium page that lists all essentiality information under that growth condition. A quantitative steady-state metabolic flux model has been derived from EcoCyc using flux balance analysis FBA [ 4748 ]. By running this model with different parameters, scientists can model the growth of E. Every time the model is executed, it is freshly generated from EcoCyc, meaning that as the reactions in EcoCyc are updated due to curation, the model automatically reflects those changes.

The Supplementary Informationprovided as the accompanying paper-suppl-info. The Supplementary Information also contains a description of the nutrient and secretion metabolite sets that supply inputs and outputs to the FBA model, as well as a description of differences between the EcoCyc FBA biomass metabolite set and the iJO WT biomass reaction.

EcoCyc provides several example files describing invocations of the FBA model under different nutrient conditions. Output files produced as a result of successful FBA runs on the supplied. The supplied input files are:. MetaFlux metabolic flux predictions from EcoCyc version O 2 uptake rates are set to an upper bound of 0.