Receptor Gene Databases

Receptor gene databases are essential for understanding cell communication networks. ReCoN provides pre-compiled receptor gene lists for human and mouse, derived from NicheNet’s prior knowledge network (PKN). These databases are used to identify receptor-ligand interactions in single-cell RNA-seq data.

Available Databases

  • Human Receptor Genes: Derived from NicheNet’s PKN.

  • Mouse Receptor Genes: Derived from NicheNet’s PKN.

Usage

To load receptor gene databases in ReCoN, use the load_receptor_genes function:

from recon.data import load_receptor_genes

# Load human receptor genes
human_receptors = load_receptor_genes("human_receptor_gene_from_NichenetPKN")

# Load mouse receptor genes
mouse_receptors = load_receptor_genes("mouse_receptor_gene_from_NichenetPKN")

These functions return a pandas DataFrame containing receptor gene information.

Integration in Tutorials

Receptor gene databases are used in the following tutorials:

  1. Predicting Treatment Effects: Identifying receptor-ligand interactions.

  2. Building GRNs with HuMMuS: Using receptor genes to infer gene regulatory networks.

For more details, refer to the respective tutorials in the documentation.