CytoSaddleSum

CytoSaddleSum integrates SaddleSum into Cytoscape to perform functional enrichment analysis using sum-of-weight scores and to represent results as term relationship networks with Cytoscape attribute annotations.

Key Features:

• SaddleSum integration: Implements SaddleSum functional enrichment analysis based on sum-of-weight scores.
• Local and remote querying: Supports local standalone queries and remote queries via HTTP requests to a web server.
• Term relationship network output: Outputs results as term relationship networks in Cytoscape where nodes represent enriched terms and edges represent relationships between those terms.
• Cytoscape attribute annotation: Writes query results as Cytoscape attributes to integrate enrichment outcomes into network datasets.

Scientific Applications:

• Functional enrichment analysis: Identify enriched biological terms from weighted node scores using sum-of-weight scoring.
• Network-based interpretation: Incorporate enrichment results into Cytoscape networks to examine term relationships and pathways.
• Network annotation for downstream analysis: Annotate networks with enrichment attributes for subsequent network-based analyses.

Methodology:

Performs enrichment scoring using SaddleSum's sum-of-weight method, supports execution locally or via HTTP to a remote web server, and generates term relationship networks while writing results as Cytoscape attributes.