SPEED

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

Key Features:

• Pathway perturbation-based annotation: Annotates genes based on their response to specific pathway perturbations rather than pathway membership.
• Signature gene identification: Identifies genes consistently regulated in single-pathway perturbation experiments as pathway-specific signatures.
• Overrepresentation detection algorithm: Detects overrepresentation of pathway signature genes within input gene lists to infer upstream signaling influences.

Scientific Applications:

• High-throughput gene-expression analysis: Infers upstream signaling pathways driving differential gene expression in high-throughput studies.
• Regulatory mechanism inference: Provides causal links between pathway perturbations and observed gene-expression changes to clarify regulatory networks.
• Disease mechanism investigation: Pinpoints signaling pathways involved in disease-related transcriptional responses.
• Therapeutic target identification: Supports prioritization of candidate pathways and biomarkers for target discovery and drug development.

Methodology:

SPEED analyzes data from single-pathway perturbation experiments to establish signature genes per signaling pathway, then assesses overrepresentation of these signatures in lists of differentially expressed genes to link expression changes to specific upstream pathways.