SEAS

SEAS performs pathway enrichment analysis by mapping bacterial gene sets to the SEED database to identify statistically enriched pathways and subsystems.

Key Features:

• Pathway Enrichment Analysis: Links differentially expressed genes or proteins to SEED pathways and subsystems to reveal functional associations.
• Gene Mapping: Maps input bacterial genes to the SEED database using gene ID and orthology mapping approaches.
• Statistical Significance Calculation: Calculates the statistical significance of enrichment for each pathway to prioritize impacted pathways.
• Organism-Specific Pathway Identification: Uses mapping strategies to identify pathways with greater organism-specific resolution compared to broader approaches.
• Reliability and Evaluation: Has been evaluated for mapping reliability, demonstrating consistent pathway association results.

Scientific Applications:

• High-throughput omics analysis: Interprets gene sets derived from high-throughput omic experiments in the context of SEED pathways and subsystems.
• Functional interpretation of differential expression: Associates differentially expressed genes or proteins with biological pathways to infer functional impacts.
• Microbial biology and pathogenesis studies: Supports investigation of microbial biology, pathogenesis, and adaptation by identifying pathway-level changes.

Methodology:

Researchers provide a set of bacterial genes, those genes are mapped to the SEED database using gene ID and orthology information, and pathway enrichment is assessed with statistical significance calculations.