CITEdb: a manually curated database of cell-cell interactions in human.

Area of Science:

• Cell Biology
• Bioinformatics
• Computational Biology

Background:

• Cell-cell interactions are crucial for organismal functions and disease.
• Single-cell technologies and data mining advance computational prediction of cell interactions.
• A systematic database for cell-type level interactions was lacking.

Purpose of the Study:

• To develop a publicly accessible database for documenting high-quality cell-cell interactions.
• To provide a benchmark dataset for evaluating computational cell-interaction prediction tools.
• To facilitate exploration of cell-cell interactions in specific physiological contexts.

Main Methods:

• Manual curation of human cell-cell interaction data.
• Development of a web interface for searching, visualizing, and downloading interaction data.
• Creation of an R package for benchmarking computational methods.

Main Results:

• Launched CITEdb (Cell-cell InTEraction database) with 728 manually curated human cell-cell interaction pairs.
• CITEdb includes structured annotations on physiological context and ligand-receptor pairs.
• The database offers interactive exploration and serves as a benchmark dataset.

Conclusions:

• CITEdb is the first database to catalogue cell-cell interactions at the cell type level.
• The database supports experimental, computational, and clinical studies of cell-cell interactions.
• CITEdb enhances the understanding and therapeutic targeting of cell communication.