A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19

Network proximity code

The proximity code can be found in the proximity/ folder. First, you need to 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

To compute the closest proximity between two gene lists

python network_proximity.py path_to_gene_list_1 path_to_gene_list_2 number_of_repeat random_seed

Example

python network_proximity.py example/Asthma.txt example/SARS2-DEG_lung.txt 1000 11096

To screen all 3000 drugs for a single gene list

python network_proximity.py DRUG path_to_gene_list number_of_repeat random_seed

Example

python network_proximity.py DRUG example/SARS2-DEG.txt 1000 1024

Please see https://github.com/ChengF-Lab/GPSnet and https://chengf-lab.github.io/PDGPS/ for more details and explanations

Visualization

👉 https://chengf-lab.github.io/COVID-19_Map/ 👈

Supplemental Files

Supplemental figures and tables are found in supplemental_files/

• S1 Table. Summary of the data sets used in this study.
• S2 Table. Five SARS-CoV-2 target data sets used in this study.
• S3 Table. Additional virus target lists for comparisons with SARS-CoV-2 targets.
• S4 Table. Disease-associated genes.
• S5 Table. COVID-19 clinical studies used in the meta-analysis.
• S6 Table. Network proximity results for 2,938 drugs against the SARS-CoV-2 data sets.
• S7 Table. Proposed repurposable drugs and their antiviral profiles.
• S1 File. Network file for the global network of disease manifestations associated with human coronavirus.