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Generic Protocol for Optimization of Heterologous Protein Production Using Automated Microbioreactor Technology

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COLOMBOS: access port for cross-platform bacterial expression compendia.

Kristof Engelen¹, Qiang Fu, Pieter Meysman

¹Department of Microbial and Molecular Systems, Katholieke Universiteit Leuven, Heverlee-Leuven, Belgium. kristof.engelen@biw.kuleuven.be

|July 23, 2011

Summary

We created cross-platform bacterial expression compendia and the COLOMBOS portal, enabling unified analysis of diverse microarray data for microbiology research.

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Area of Science:

Microbiology
Bioinformatics
Systems Biology

Background:

Microarray data heterogeneity limits public database utility.
Bacterial expression compendia are scarce and platform-specific.
Existing resources lack direct integration of diverse experimental data.

Purpose of the Study:

To develop organism-specific, cross-platform expression compendia for bacterial model organisms.
To create an integrated access portal (COLOMBOS) for compendia analysis.
To facilitate the exploration of heterogeneous microarray data.

Main Methods:

Directly combined gene expression data from different microarray platforms and experiments.
Developed the COLOMBOS portal with integrated analysis and visualization tools.
Incorporated extensive gene and experimental condition annotations.

Main Results:

Constructed comprehensive expression compendia for Escherichia coli, Bacillus subtilis, and Salmonella enterica serovar Typhimurium.
The COLOMBOS portal provides access to compendia and analysis tools.
Demonstrated utility by extending the known regulon of the Fur transcription factor in E. coli.

Conclusions:

Created valuable cross-platform bacterial expression compendia and the COLOMBOS analysis tool.
Facilitates the extraction of biological insights from public microarray data.
Supports the microbiology research community by enhancing data accessibility and usability.