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ProGenExpress: visualization of quantitative data on prokaryotic genomes.

Michael Watson1

  • 1Institute for Animal Health, Compton laboratory, High street, Compton, Newbury, RG20 7NN, UK. michael.watson@bbsrc.ac.uk

BMC Bioinformatics
|April 15, 2005
PubMed
Summary

ProGenExpress is a new R package for visualizing quantitative experimental data within prokaryotic genomes. It aids in analyzing complex datasets and identifying novel regions of interest in microbial systems biology.

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Area of Science:

  • Systems Biology
  • Genomics
  • Bioinformatics

Background:

  • Systems biology integrates genomic data with experimental results.
  • Sequencing microbial genomes generates vast post-genomics data.
  • Prokaryotic genomes contain structures like operons, pathogenicity islands, and prophage sequences relevant to disease.

Purpose of the Study:

  • To develop a novel tool for visualizing complex numerical data within the context of prokaryotic genomes.
  • To provide a simple and effective method for analyzing integrated genomic and experimental datasets.

Main Methods:

  • Development of ProGenExpress, an R package.
  • Utilizing ProGenExpress to visualize quantitative measurements (e.g., microarray, proteomics data) on prokaryotic genome organization.

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  • Implementing search functionality for novel regions of interest based on gene patterns in experimental data.

    • Main Results:

    • ProGenExpress enables easy and quick visualization of quantitative measurements in prokaryotic genomes.
    • The package accurately displays data from whole-genome technologies like microarrays and proteomics.
    • ProGenExpress successfully identified novel regions of interest in a Salmonella typhimurium time-course experiment.

    Conclusions:

    • ProGenExpress is a valuable tool for visualizing quantitative data in the context of sequenced prokaryotic genomes.
    • The package facilitates the discovery of novel regions of interest from complex experimental datasets.