Related Experiment Video
Updated: Jan 16, 2026
A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
Published on: July 1, 2020
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.
Motivation:
Pathways are biological networks describing interactions between genes, proteins, non-coding RNAs, drugs and chemical compounds that contribute to develop a specific metabolic function or biological process. Identifying perturbed pathways associated with a phenotype or condition helps to understand how functional processes are altered in complex diseases and which genes play a key role in these alterations. Recently, several algorithms have been developed to identify perturbed pathways associated with a phenotype. Still, no tools are available to visualize and compare perturbed pathways in the same species or different organisms.
Results:
Here, we present a web app called PAthway COmparator (PACO) to compare two or more sets of altered pathways associated with different phenotypes, starting from either custom data or simulation data returned by the pathway analysis algorithms MITHrIL and PHENSIM. The app allows users to visualize and compare the altered pathways, and zoom into specific regions. We show the potential applicability of PACO through a case study in which perturbed immune system pathways are compared in mice and humans after up-regulation of Interferon-stimulated gene 15 (ISG15).
Availability And Implementation:
PACO is implemented as a Shiny R web application and is available at https://paco.dioncogen.eu/.
Insights
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.
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.
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