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CAT-GxD: Centralized access to gene expression datasets.

Bryan Angelo P Roxas¹, Jennifer Lising Roxas¹, Jessica S Guo²

¹School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA.

|October 15, 2025

Summary

This summary is machine-generated.

Researchers can now easily analyze bacterial gene expression data using the new Centralized Access to Gene Expression Datasets (CAT-GxD) search engine. This tool simplifies access to multi-omic data for Clostridioides difficile, aiding hypothesis generation and target identification.

Keywords:

Bacterial gene expression datasets Clostridioides difficile Database Multi-omic Proteomics Transcriptomics

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Area of Science:

Microbiology
Bioinformatics
Genomics

Background:

Publicly available bacterial gene expression datasets are extensive but difficult to access and analyze due to complexity and specialized expertise requirements.
Limited tools exist to unify and interpret multi-omic datasets, hindering research and hypothesis testing.

Purpose of the Study:

To develop an integrated search engine, CAT-GxD, simplifying access to and analysis of publicly available bacterial gene expression data.
To facilitate comparison and hypothesis-driven research using multi-omics datasets.

Main Methods:

Developed the Centralized Access to Gene Expression Datasets (CAT-GxD) search engine using R-shiny.
Manually curated and standardized 74 transcriptomics and proteomics datasets for Clostridioides difficile from GEO and ProteomeXchange.
Integrated disparate datasets for unified access and analysis.

Main Results:

CAT-GxD successfully consolidated transcriptomics and proteomics data for Clostridioides difficile.
The search engine offers customizable visualizations of gene expression data under various conditions.
Demonstrated utility in analyzing RpoN regulation in C. difficile, including responses to succinate and deoxycholate.

Conclusions:

CAT-GxD streamlines multi-omic data analysis for C. difficile, reducing complexity and time.
The tool facilitates novel hypothesis generation and identification of anti-infective targets.
CAT-GxD is adaptable for diverse organisms and data analysis paradigms.