SPEED

SPEED identifies upstream signaling pathways responsible for differential gene expression by enrichment analysis of pathway-specific signature genes derived from single-pathway perturbation experiments.

Key Features:

• Causal pathway identification: Focuses on pinpointing signaling pathways that cause gene expression changes rather than on protein membership in pathways.
• Signature gene identification: Identifies signature genes unique to specific signal transduction pathways that serve as biomarkers of pathway activity.
• Perturbation-derived signatures: Uses consistently regulated genes derived from single-pathway perturbation experiments to define pathway signatures.
• Algorithmic overrepresentation detection: Applies a specialized algorithm to assess overrepresentation of signature genes within an input gene group to infer active upstream pathways.

Scientific Applications:

• Disease mechanism elucidation: Infers signaling pathways contributing to disease-associated differential gene expression to inform therapeutic target identification and drug development.
• Developmental pathway analysis: Analyzes pathway-driven gene regulation in developmental biology studies.
• Comparative genomics: Identifies conserved pathway activities across conditions or species by comparing signature enrichment.

Methodology:

Signature genes are derived from single-pathway perturbation experiments, signature genes unique to signal transduction pathways are identified, and a specialized algorithm assesses overrepresentation of these signature genes within an input gene set.