Neuro-immune interactome

This repository accompanies the manuscript "Nociceptor neuroimmune interactomes reveal common and injury-specific inflammatory pain pathways" and contains code to generate the interactome.

The Python script to generate the interactome is at interactome/core.py. Output files, including gene lists and generated CellPhoneDB input interaction tables are in the output folder.

In the output/cpdb folder, interactome files using UniProt IDs are provided:

• ligand_receptor_unique_interactions.csv
• ligand_ion_channel_interactions.csv
• enzyme_product_unique_interactions.csv

which are used as input to CellPhoneDB. In addition, versions of these interactome files that use gene names

• enzyme_product_unique_interactions_hgnc.csv
• ligand_ion_channel_unique_interactions_hgnc.csv
• ligand_receptor_unique_interactions_hgnc.csv

are also provided for convenience. Finally, the merged interactome is available both using UniProt IDs and using gene names:

• all_interactions.csv
• all_interactions_hgnc.csv