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Functional Complementation Analysis FCA: A Laboratory Exercise Designed and Implemented to Supplement the Teaching of Biochemical Pathways

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ESKAPE Act Plus: Pathway Activation Analysis for Bacterial Pathogens.

Katja Koeppen¹, Thomas H Hampton¹, Samuel L Neff¹

¹Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.

|October 19, 2022

Summary

This summary is machine-generated.

ESKAPE Act PLUS is a new web tool for analyzing bacterial gene expression data. It helps researchers understand how experimental conditions affect prokaryotic biological functions and pathways, aiding research on antibiotic-resistant pathogens.

Keywords:

ESKAPE ESKAPE pathogens GO terms KEGG Prokaryotes Shiny Shiny web application bacteria gene ontology pathogens pathway activation analysis prokaryotes web application

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Area of Science:

Microbiology and Bioinformatics
Genomics and Proteomics

Background:

The increasing volume of gene expression and proteomic data requires advanced analytical tools.
Existing tools often have limitations for prokaryotic research, creating a gap in functional analysis capabilities.

Purpose of the Study:

To introduce ESKAPE Act PLUS, a novel Shiny web application designed to bridge the gap in functional analysis tools for prokaryotic gene and protein expression data.
To provide researchers with a user-friendly platform for analyzing high-throughput bacterial expression experiments.

Main Methods:

Development of a Shiny web application, ESKAPE Act PLUS.
Implementation of statistical approaches for pathway activation analysis without requiring pre-identification of differentially expressed genes.
Integration of KEGG pathway and Gene Ontology (GO) term analysis.

Main Results:

ESKAPE Act PLUS analyzes gene or protein expression data from 13 bacterial species, including ESKAPE pathogens.
The tool provides identification of significantly activated or repressed KEGG pathways and GO terms.
It generates visual representations of pathway activation/repression and detailed pathway diagrams with gene fold changes.

Conclusions:

ESKAPE Act PLUS offers unique pathway activation analysis and visualization for prokaryotes, advancing research on bacterial pathogens.
The application facilitates the inference of biological phenotypes from expression data, supporting hypothesis generation for future experiments.
This tool enhances the study of ESKAPE pathogens and other bacteria relevant to the biomedical community.