GSOAP

GSOAP visualizes gene set over-representation analysis (GSOA) results by mapping relationships among enriched instances and highlighting significance, closeness centrality, and clustering to support interpretation of pathway and functional-category enrichment.

Key Features:

• GSOA visualization: Provides visual representations of gene set over-representation analysis (GSOA) results showing overlaps between gene sets and enriched instances.
• Relationship mapping: Illustrates relationships among enriched instances to reveal interconnectedness.
• Significance highlighting: Encodes and emphasizes statistical significance of enrichment results.
• Centrality (closeness): Emphasizes closeness centrality as a measure of instance centrality within the relationship map.
• Clustering: Highlights clustering of enriched instances to reveal modules or groups of related terms.
• Supported instance types: Applies to enriched instances such as biological pathways and functional categories.
• Implementation: Implemented as an R package.

Scientific Applications:

• Pathway analysis: Aids interpretation of enriched biological pathways by visualizing relationships and significance among pathway terms.
• Functional genomics: Supports exploration of functional-category enrichment for gene sets derived from genomic experiments.
• Systems biology: Reveals interconnected functional modules and central entities within enriched instance networks for systems-level interpretation.

Methodology:

Implemented as an R package that generates visualizations illustrating relationships among enriched instances while emphasizing significance, closeness centrality, and clustering.