YPIBP

YPIBP catalogs phosphoinositide-binding proteins in yeast and compiles curated data on 679 PI-binding proteins, their lipid specificities, and domain annotations to support analyses of phosphoinositide–protein interactions.

Key Features:

• Curated protein set: 679 phosphoinositide-binding proteins compiled from high-throughput proteome-array and lipid-array studies, QuickGO annotations, and literature mining.
• Domain classification: Protein domains are annotated and categorized into lipid-binding domains, lipid-related domains, and other relevant domains.
• Enrichment analyses: PI-binding enrichment analysis and domain enrichment analysis identify significant associations within the dataset.
• PI-domain-protein interactome mapping: Representation of interactions among phosphoinositides, domains, and proteins derived from the aggregated dataset.
• Case studies: Three case studies illustrate analytical applications for investigating PI–protein relationships.

Scientific Applications:

• Lipid signaling and membrane trafficking: Analysis of roles of phosphoinositides—including phosphatidylinositol (PtdIns) and its seven phosphorylated derivatives—in lipid signaling, protein transport, and membrane trafficking in yeast.
• Domain-function inference: Investigation of domain-based mechanisms underlying lipid–protein interactions by linking domain annotations to PI-binding data.
• Enrichment-driven hypothesis generation: Identification of statistically enriched proteins, domains, or PI interactions for experimental follow-up using enrichment analyses.

Methodology:

Proteins were collected from high-throughput proteome-array and lipid-array studies, QuickGO annotations, and literature mining; domains were annotated and classified into lipid-binding, lipid-related, and other categories; PI-binding enrichment analysis and domain enrichment analysis were applied.