PlantPhoneDB

PlantPhoneDB provides a pan-plant database of curated high-confidence ligand–receptor pairs to enable inference of cell–cell communication from single-cell RNA-sequencing (scRNA-seq) data.

Key Features:

• Manually Curated Data: High-confidence ligand–receptor pairs curated from seven distinct resources are aggregated for pan-plant coverage.
• Integration with scRNA-seq: Uses single-cell RNA-sequencing (scRNA-seq) expression patterns to associate ligands and receptors for inferring intercellular communication.
• PlantPhoneDB R Package: Implements four distinct scoring approaches to calculate interaction scores between cell types and provides visualization tools for results.

Scientific Applications:

• Discovery of plant cell–cell communication: Enables identification of novel cell–cell communication events from plant scRNA-seq datasets.
• Arabidopsis thaliana heat-shock analysis: Application to GSE121619 predicted active communication of ligand–receptor pair AT1G28290-AT2G14890 between atrichoblast and cortex cell pairs, linked to the ribosome pathway during heat response.

Methodology:

Integration and manual curation of ligand–receptor pairs from seven resources, leveraging scRNA-seq expression patterns to infer interactions, with an R package implementing four scoring approaches and visualization tools.