Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

The EcoCyc Database.

Peter D Karp1, Monica Riley, Milton Saier

  • 1Bioinformatics Research Group, SRI International, 333 Ravenswood Avenue EK207, Menlo Park, CA 94025, USA. pkarp@ai.sri.com

Nucleic Acids Research
|December 26, 2001
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

One Yeast, Sixteen Synthetic Chromosomes, Infinite Possibilities.

Yeast (Chichester, England)·2026
Same author

Synthesis of Programmable Bioelectronic Yeast for Biohybrid Futures.

Engineering biology·2026
Same author

Fine-tuned GPT-based foundation models effectively reconstruct bacterial transcriptional regulatory networks from literature.

Frontiers in artificial intelligence·2026
Same author

Environment and Pollen Diversity Differentially Affect the Gut Microbiomes of Introduced Honeybees and Bumblebees.

Evolutionary applications·2026
Same author

Agriculture alters protein evolution of respiratory nitrate reductase in soil bacteria at a global scale.

Environmental research·2026
Same author

Marine heatwaves alter shell microbiomes and denitrification capacity: An oyster family-specific response.

Marine pollution bulletin·2026
Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026
See all related articles

EcoCyc is a comprehensive database detailing the metabolic and signal-transduction pathways of Escherichia coli. It provides insights into enzymes, transport proteins, and gene expression control, accessible via Pathway Tools.

Area of Science:

  • Microbiology and Bioinformatics
  • Systems Biology
  • Genomics and Proteomics

Background:

  • Understanding cellular processes in model organisms like Escherichia coli is crucial for biological research.
  • Metabolic and signal-transduction pathways are fundamental to cellular function and regulation.
  • Efficient access to curated genomic and pathway data is essential for researchers.

Purpose of the Study:

  • To present EcoCyc, an organism-specific pathway/genome database for Escherichia coli.
  • To describe the comprehensive data content within EcoCyc, including metabolic pathways, enzymes, transport proteins, and transcriptional control mechanisms.
  • To highlight the utility of the Pathway Tools graphical user interface for querying and visualizing EcoCyc data.

Main Methods:

Related Experiment Videos

  • Development and curation of an organism-specific pathway/genome database (EcoCyc).
  • Integration of data on metabolic pathways, enzymes, transport proteins, and transcriptional regulation for Escherichia coli.
  • Implementation of the Pathway Tools graphical user interface for data access and analysis.

    • Main Results:

    • EcoCyc provides a detailed description of Escherichia coli's metabolic and signal-transduction pathways.
    • The database includes comprehensive information on enzymes, transport proteins, and gene expression control mechanisms.
    • The Pathway Tools interface facilitates diverse query operations and visualization of pathway and genomic data.

    Conclusions:

    • EcoCyc serves as a valuable, integrated resource for studying the biology of Escherichia coli.
    • The database and its associated tools enable in-depth analysis of cellular pathways and genetic regulation.
    • EcoCyc is readily accessible online, promoting wider research application.