gsean

gsean implements network-informed Gene Set Enrichment Analysis (GSEA) in R/Bioconductor by constructing a gene co-expression network from the input expression matrix to refine enrichment calculations and provide a systems-level perspective on pathway and gene-set activity.

Key Features:

• R/Bioconductor implementation: Provided as an R/Bioconductor package for integration with Bioconductor workflows and data structures.
• Network construction: Constructs a biological network, typically a gene co-expression network, directly from the input expression matrix.
• Network-informed enrichment: Incorporates derived network topology into GSEA to refine enrichment calculations and account for coordinated gene behavior.
• Regulatory and co-expression capture: Captures regulatory structure, co-expression patterns, and functional modules that are lost in gene-independent analyses.
• Systems-level interpretation: Provides a systems-level perspective on functional activity and pathway activation patterns.
• Improved precision and interpretability: Enhances the precision and interpretability of enrichment results for processes driven by gene–gene interactions.
• Interaction-driven pathway detection: Identifies pathways or gene sets whose activity emerges from structured interactions rather than marginal changes in single genes.

Scientific Applications:

• Systems biology: Analyzing pathway activation and module activity in systems biology studies.
• Regulatory network inference: Interpreting regulatory network signals by integrating co-expression topology into enrichment analysis.
• High-dimensional transcriptomic analysis: Detecting pathway-level signals in high-dimensional transcriptomic datasets that are not evident at the single-gene level.
• Pathway activity detection: Revealing pathway activation patterns that traditional list-based enrichment approaches may miss.

Methodology:

Derives network topology from the expression data by constructing a gene co-expression network from the input expression matrix and incorporates that topology into Gene Set Enrichment Analysis to refine enrichment calculations.