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Updated: May 10, 2026
03:08
Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
Published on: October 3, 2025
Inferring the functional effect of gene expression changes in signaling pathways
Patricia Sebastián-León1, José Carbonell, Francisco Salavert
1Department of Computational Genomics, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain.
Nucleic Acids Research
|June 11, 2013
Summary
PATHiWAYS is a new web tool that visualizes signaling pathways. It helps identify key signaling circuits linked to specific biological problems using gene expression data.
Area of Science:
- Molecular Biology
- Bioinformatics
- Systems Biology
Background:
- Signaling pathways are crucial for understanding cell functionality and gene activity.
- Existing tools allow pathway visualization and data representation, but lack methods for identifying specific signaling circuits related to biological problems.
- There is a need for user-friendly graphical web interfaces for analyzing signaling pathway alterations.
Purpose of the Study:
- To present PATHiWAYS, a web-based system for visualizing signaling pathways.
- To infer changes in signaling that affect cell functionality from gene expression data.
- To provide a graphical web interface for identifying signaling circuits associated with biological problems.
Main Methods:
- Utilizes a probabilistic model of signaling pathways.
- Infers probabilities of signal transmission from receptors to effector molecules based on pathway topology.
- Estimates gene product presence/absence probabilities from gene expression microarray data.
Main Results:
- Identifies significant changes in signal transmission probabilities.
- Links specific cell functionalities triggered by pathways to the studied biological problem.
- Provides a web-based graphical visualization system (PATHiWAYS).
Conclusions:
- PATHiWAYS enables the identification of critical signaling circuits within pathways.
- The system effectively links gene expression changes to cellular functions and biological contexts.
- Offers a valuable tool for researchers studying signaling pathway alterations in case-control experiments.
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