EchoBASE

EchoBASE aggregates and integrates experimental and bioinformatic data for Escherichia coli K-12 strain MG1655 to support characterization of approximately 1,500 uncharacterized gene products and orphan enzyme activities.

Key Features:

• Relational database: Manages and integrates diverse experimental and bioinformatic datasets tied to E. coli K-12 MG1655.
• Genome-based annotation framework: Uses an enhanced annotation framework based on the updated MG1655 genome sequence to link annotations to genes and gene products.
• Supported experimental types: Incorporates proteomics, microarray, protein-protein interaction, structural biology, and other bioinformatics datasets.
• Orphan enzyme curation: Curates annotated information about enzymes lacking confirmed biochemical reactions.
• Gene–product association: Associates multiple experimental data types with specific genes and their corresponding products.
• Uncharacterized gene target set: Focuses on a set of approximately 1,500 gene products that currently lack confirmed cellular roles.

Scientific Applications:

• Orphan enzyme characterization: Facilitates identification and study of proteins that catalyze unknown biochemical reactions in E. coli.
• Functional annotation of genes: Supports assignment of cellular roles to uncharacterized gene products and hypothesis generation for gene function.
• Post-genomic integrative analyses: Provides integrated datasets for post-genomic studies of bacterial cellular functions and biochemical pathways.
• Structural and interaction mapping: Enables correlation of structural biology and protein–protein interaction data with gene annotations.

Methodology:

Relational database integration of experimental datasets linked to the updated MG1655 genome annotations, with curation of annotations for orphan enzyme activities and association of proteomics, microarray, protein–protein interaction, structural biology, and other bioinformatics datasets to gene products.