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EchoBASE: an integrated post-genomic database for Escherichia coli.

Raju V Misra1, Richard S P Horler, Wolfgang Reindl

  • 1Department of Biology (Area 10), University of York, PO Box 373,York, YO10 5YW, UK.

Nucleic Acids Research
|December 21, 2004
PubMed
Summary

EchoBASE is a new relational database for Escherichia coli K-12 post-genomic experiments. It aims to identify functions for 1500 uncharacterized gene products using integrated experimental data.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • The model bacterium Escherichia coli K-12 has numerous gene products with unknown functions.
  • Post-genomic experimental data is often dispersed across various sources, hindering comprehensive analysis.

Purpose of the Study:

  • To create a centralized relational database, EchoBASE, for managing and analyzing Escherichia coli K-12 experimental data.
  • To aid in the functional characterization of approximately 1500 Escherichia coli K-12 gene products with no confirmed cellular function.

Main Methods:

  • Developed EchoBASE, a relational database integrating enhanced genome annotation of E. coli K-12 strain MG1655.
  • Associated diverse experimental data, including proteomics, microarray, protein-protein interactions, structural, and bioinformatics studies, with E. coli genes and products.

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  • Incorporated annotated information on 'orphan' enzyme activities to assist in protein characterization.

    • Main Results:

    • EchoBASE provides a unified platform for accessing and manipulating a wide range of experimental data related to E. coli K-12.
    • The database facilitates the investigation of gene product functions by linking experimental evidence to genomic information.
    • Annotated 'orphan' enzyme activities within EchoBASE offer starting points for understanding novel biochemical pathways.

    Conclusions:

    • EchoBASE serves as a valuable resource for the Escherichia coli research community, accelerating functional genomics studies.
    • The integrated approach aids in deciphering the roles of uncharacterized proteins and enzymes.
    • This database supports the broader goal of understanding the complete functional landscape of E. coli K-12.