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Using a Bacterial Pathogen to Probe for Cellular and Organismic-level Host Responses
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Co-PATHOgenex web application for assessing complex stress responses in pathogenic bacteria.

Leyden Fernandez1,2,3, Martin Rosvall3, Johan Normark2,4

  • 1Department of Molecular Biology, Umeå Centre for Microbial Research (UCMR), Umeå University , Umeå, Sweden.

Microbiology Spectrum
|November 29, 2023
PubMed
Summary
This summary is machine-generated.

We developed Co-PATHOgenex, a web tool for building bacterial gene co-expression networks. This application helps researchers understand pathogen adaptation and identify novel gene functions under stress conditions.

Keywords:
RNA-seqbacterial pathogensgene co-expressiongene regulationstimulonstress responsestranscriptomics

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Systems Biology

Background:

  • Understanding bacterial adaptive strategies within hosts is crucial.
  • Gene co-expression networks offer insights into bacterial gene regulation and function.
  • Existing tools may lack user-friendliness or specific features for pathogen analysis.

Purpose of the Study:

  • To develop an interactive web application, Co-PATHOgenex, for constructing gene co-expression networks in bacterial pathogens.
  • To provide a user-friendly platform with integrated search and visualization tools for network analysis.
  • To incorporate stress stimulons for identifying novel gene-stress associations.

Main Methods:

  • Development of a web application (Co-PATHOgenex) using Shiny.
  • Implementation of user-defined thresholds for network construction.
  • Integration of search functionalities and interactive visualizations.
  • Inclusion of pre-compiled stress stimulon data for selected bacterial species.

Main Results:

  • Co-PATHOgenex enables the construction and visualization of bacterial gene co-expression networks.
  • The tool simplifies the interpretation of complex network data through intuitive features.
  • Stress stimulons within Co-PATHOgenex facilitate the discovery of genes linked to specific stress responses.

Conclusions:

  • Co-PATHOgenex is a valuable resource for researchers studying bacterial pathogen adaptation.
  • The application enhances the exploration of gene function and regulatory mechanisms.
  • It aids in identifying potential virulence factors and novel therapeutic targets.