pathDIP

pathDIP integrates curated pathways from 24 major pathway databases with predicted pathway associations derived from orthology and protein–protein interactions (PPIs) to extend pathway annotation and enable pathway enrichment analysis across human, model organisms, and domesticated species.

Key Features:

• Cross-species coverage: Comprehensive pathway annotations across human, model organisms, and domesticated species.
• Database integration: Integration of core pathways from 24 major curated pathway databases.
• PPI-based prediction: Prediction of protein–pathway associations using protein–protein interaction (PPI) networks.
• Orthology-based projection: Projection of pathway annotations across species based on orthology relationships.
• Proteome annotation extent: Extends human proteome annotation coverage to 92%.
• Human annotation count: Annotation of 5,366 pathway or kości for humans.
• Total pathways: Includes 6,401 core and predicted pathways.
• Curation and prediction integration: Combines manually curated entries with computational predictions derived from sequence homology and functional enrichment analyses.
• Signaling cascades: Annotated signaling cascades integrated with curated and predicted pathway entries.

Scientific Applications:

• Functional genomics: Supports functional interpretation of gene and protein sets through pathway annotations and enrichment.
• Systems biology: Facilitates systems-level analysis of signaling and interaction networks within pathway context.
• Comparative pathway analysis: Enables comparison of pathway annotations across human, model organisms, and domesticated species.
• Pathway enrichment analysis: Supports enrichment analyses using integrated curated and predicted pathway sets.

Methodology:

Integrates core pathways from curated pathway databases and predicts protein–pathway associations using orthology, protein–protein interaction (PPI) networks, sequence homology, and functional enrichment analyses.