CITEdb

CITEdb documents 728 high-quality human cell-cell interactions at the cell type level, annotated with ligand-receptor pairs and physiological contexts to support experimental and computational studies of cellular communication.

Key Features:

• Manual curation: Contains 728 manually curated cell-cell interaction pairs annotated with physiological contexts such as specific diseases or organs and the ligand-receptor pairs mediating each interaction.
• Annotation of ligand-receptor pairs: Records ligand-receptor relationships connecting specific cell types to enable analysis of signaling mechanisms at the cell-type level.
• Benchmark dataset and tools: Serves as a benchmark dataset for evaluating computational predictions of cell-cell interactions and includes an R package implementing the benchmark functionality.

Scientific Applications:

• Experimental validation: Supports experimental studies that validate cell-cell interactions and their physiological contexts.
• Computational benchmarking: Enables evaluation and comparison of computational tools that predict cell-cell interactions from single-cell data.
• Disease and therapeutic research: Facilitates investigation of cell-cell communication in cancers and other diseases to inform potential therapeutic interventions.

Methodology:

CITEdb leverages recent advancements in single-cell technologies and data mining methods to computationally predict cell-cell interactions, and these predictions are then systematically documented and curated within the database.