ShinyDegSEM: an interactive application for pathway perturbation analysis in gene expression studies via structural...

Area of Science:

• Bioinformatics
• Systems Biology
• Genomics

Background:

• Understanding phenotypic variation requires dissecting complex biological pathways and gene regulatory networks.
• Identifying perturbed pathways and their propagation is a key challenge in biological research.

Purpose of the Study:

• To introduce ShinyDegSEM, an interactive R Shiny application for pathway perturbation analysis in gene expression studies.
• To provide a user-friendly tool for identifying differentially expressed genes (DEGs) and uncovering perturbed pathway modules using structural equation modeling (SEM).

Main Methods:

• Utilizes SEM for pathway perturbation analysis.
• Integrates DEG detection (Significance Analysis of Microarray) and pathway analysis (Signaling Pathway Impact Analysis).
• Features an interactive interface for data upload, analysis parameter selection, and result visualization.

Main Results:

• ShinyDegSEM facilitates the identification of DEGs and the construction of pathway models.
• The tool enables evaluation of these models to pinpoint perturbed pathway modules.
• Provides insights into deregulated genes and altered gene-gene relationships within pathways.

Conclusions:

• ShinyDegSEM streamlines pathway perturbation analysis for gene expression data.
• The application empowers researchers, including novices, to explore complex gene regulatory mechanisms.
• Offers a comprehensive workflow from DEG detection to SEM-based model refinement and comparison.