EcoCyc
Category Cross-Omics>Knowledge Bases/Databases/Tools
Abstract EcoCyc (Encyclopedia of Escherichia coli Genes and Metabolism) is a bioinformatics database that describes the genome and the biochemical machinery of E. coli.
The long-term goal of the project is to describe the molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli.
EcoCyc is an electronic reference source for E. coli biologists, and for biologists who work with related microorganisms.
Products features/capabilities include:
1) Genome -- EcoCyc contains the complete genome sequence of E. coli, and describes the nucleotide position and function of every E. coli gene. A staff of five (5) full-time curators updates the annotation of the E. coli genome on an ongoing basis using a literature-based curation strategy.
Minireview summaries of E. coli gene products can be found in EcoCyc protein and RNA pages. Users can retrieve the nucleotide sequence of a gene, and the amino-acid sequence of a gene product.
2) Regulation -- EcoCyc describes several types of E. coli cellular regulation:
- a) Substrate-level enzyme regulation - Provided for hundreds of E. coli enzymes.
- b) Transcriptional regulation - EcoCyc contains the most complete description of the genetic network of any organism, including E. coli operons, promoters, transcription factors and transcription-factor binding sites.
- The transcriptional regulatory information in the EcoCyc and RegulonDB databases are both curated by the group of Dr. Julio Collado-Vides at the National Autonomous University of Mexico (UNAM), and that the databases therefore contain the same data content on 'transcriptional regulation' of gene expression.
- Actual curation of the data occurs within EcoCyc, and is periodically propagated to RegulonDB.
- c) Attenuation - Curation of regulation by attenuation began in 2008.
- d) Regulation by small RNAs - Curation of small RNA based regulation began in 2008.
3) Membrane transporters -- The project is annotating E. coli transport proteins and the associated transport reactions that they mediate.
4) Metabolism -- EcoCyc describes all known metabolic pathways and signal-transduction pathways of E. coli. It describes each metabolic enzyme of E. coli, including its cofactors, activators, inhibitors, and subunit structure.
See also the MetaCyc project (see G6G Abstract Number 20232).
5) Database links -- EcoCyc is linked to other biological databases containing protein and nucleic-acid sequence data, bibliographic data, protein structures, and descriptions of different E. coli strains.
6) Literature-Based Curation -- 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 April 2008, EcoCyc has encoded information from more than 16,000 publications.
7) Query and Visualization -- Scientists can use the 'BioCyc Query Page' or a 'downloadable program' to visualize the layout of genes within the E. coli chromosome, or of an individual biochemical reaction, or of a complete biochemical pathway (with compound structures displayed).
The navigation capabilities of the software allow a user to move from a display of an enzyme to a display of a reaction that the enzyme catalyzes or to the gene that encodes the enzyme.
8) Analysis of Omics Data -- EcoCyc provides software tools for the analysis of Omics datasets:
- a) The 'Pathway Tools Omics Viewer' (see G6G Abstract Number 20237) allows metabolomics, gene expression, and proteomics data to be painted on a complete E. coli metabolic pathway map.
- b) The Pathway Tools Omics Viewer allows omics datasets to be painted onto the E. coli regulatory network.
- c) The Pathway Tools Omics Viewer allows omics datasets to be visualized against the full E. coli genome map.
- d) The Genome Browser tracks allow ChIP-chip data, and other positional data, to be viewed against regions of the E. coli genome.
System Requirements
See G6G Abstract Number 20230 or BioCyc
Manufacturer
- Bioinformatics Research Group
- Dr Peter D Karp
- Director, Bioinformatics Research Group
- Artificial Intelligence Center
- SRI International
- 333 Ravenswood Avenue
- Menlo Park, CA 94025-3493
- Phone: (650) 859-2000
- ptools-info@ai.sri.com
- biocyc-support@ai.sri.com
Manufacturer Web Site EcoCyc
Price Contact manufacturer.
G6G Abstract Number 20231
G6G Manufacturer Number 102506