Transcriptomics-based Network Medicine Discovery and Population-based Validation Identifies Metformin as a Candidate Drug for Atrial Fibrillation
The proximity code can be found in the proximity/
folder. First, decompress the file HumanInteractome.7z
in the same folder.
- HumanInteractome.tsv - the human interactome, including sources and evidence types
- HumanInteractome.npy - numpy matrix of all precalculated shortest distance in the interactome
- DrugTargetNetwork.txt - drug target network
- network_proximity.py - code to compute closest network proximity. See below
The network_proximity.py
supports two modes. To run the program (Python 3), numpy and networkx need to be installed.
pip install numpy networkx
python network_proximity.py path_to_gene_list_1 path_to_gene_list_2 number_of_repeat random_seed
python network_proximity.py DRUG path_to_gene_list number_of_repeat random_seed
Save the gene Entrez IDs in a single column, e.g.,
58
162
166
310
373
396
409
427
476
481
514