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PACO: a Shiny app for comparing perturbed pathways associated with different phenotypes.

Giovanni Micale1, Salvatore Alaimo1, Alfredo Pulvirenti1

  • 1Department of Clinical and Experimental Medicine, University of Catania, Catania, 95123, Italy.

Bioinformatics Advances
|September 26, 2025
PubMed
Summary
This summary is machine-generated.

PAthway COmparator (PACO) is a new web app for visualizing and comparing altered biological pathways. This tool aids in understanding complex diseases by comparing pathway perturbations across species.

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Area of Science:

  • Systems Biology
  • Bioinformatics
  • Genomics

Background:

  • Biological pathways are networks of molecular interactions crucial for cellular functions.
  • Identifying altered pathways is key to understanding complex diseases and gene roles.
  • Current tools lack the ability to visualize and compare perturbed pathways across species.

Purpose of the Study:

  • To introduce PAthway COmparator (PACO), a novel web application for pathway analysis.
  • To enable visualization and comparison of altered pathways associated with different phenotypes.
  • To facilitate cross-species pathway comparison.

Main Methods:

  • PACO is developed as a Shiny R web application.
  • It accepts custom data or simulation data from pathway analysis algorithms (MITHrIL, PHENSIM).
  • The application allows users to visualize, compare, and zoom into specific pathway regions.

Main Results:

  • PACO enables the comparison of perturbed pathways across different phenotypes and species.
  • A case study demonstrated PACO's utility by comparing immune system pathways in mice and humans.
  • The comparison focused on alterations following Interferon-stimulated gene 15 (ISG15) up-regulation.

Conclusions:

  • PACO addresses the need for tools to visualize and compare altered pathways.
  • The application supports comparative pathway analysis within and across species.
  • PACO is a valuable resource for researchers studying complex diseases and comparative genomics.