Specifying information sources

In this example, the sources of information in the network are proteins that have interactions with SARS-CoV-2 proteins.

import os, sys
import numpy as np
import scipy as sp
import pandas as pd

import math

import networkx as nx
import matplotlib.pyplot as plt

from neo4j import GraphDatabase, basic_auth
from CoRe.cypher_commands import command_set
from CoRe.ncip import ncip

import json

Read SARS-CoV2 proteins and human proteins that have protein-protein interaction

data_directory = "./Examples"
os.chdir(data_directory)

data = pd.read_csv('SARS-Cov2_proteins.csv')

Cov2_proteins = data['Bait'].to_list()

interaction_proteins = data['PreyGene'].to_list()

SARS_CoV2_pnames = pd.read_csv('ordered_SARS-CoV-2_proteins.csv')['Bait'].to_list()
print(SARS_CoV2_pnames)

CoV2_interactions = {}

for CoV2_protein in SARS_CoV2_pnames:
    CoV2_interactions[CoV2_protein] = []

for a,b in zip(Cov2_proteins,interaction_proteins):
    CoV2_interactions[a].append(b)

json_obj = json.dumps(CoV2_interactions)
f = open('SARS_CoV2-interactions.json','w')
f.write(json_obj)
f.close()

['SARS-CoV2 Nsp1', 'SARS-CoV2 Nsp2', 'SARS-CoV2 Nsp3', 'SARS-CoV2 Nsp4', 'SARS-CoV2 Nsp5', 'SARS-CoV2 Nsp5_C145A', 'SARS-CoV2 Nsp6', 'SARS-CoV2 Nsp7', 'SARS-CoV2 Nsp8', 'SARS-CoV2 Nsp9', 'SARS-CoV2 Nsp10', 'SARS-CoV2 Nsp11', 'SARS-CoV2 Nsp12', 'SARS-CoV2 Nsp13', 'SARS-CoV2 Nsp14', 'SARS-CoV2 Nsp15', 'SARS-CoV2 Spike', 'SARS-CoV2 ORF3a', 'SARS-CoV2 ORF3b', 'SARS-CoV2 E', 'SARS-CoV2 M', 'SARS-CoV2 ORF6', 'SARS-CoV2 ORF7a', 'SARS-CoV2 ORF8', 'SARS-CoV2 ORF9b', 'SARS-CoV2 ORF9c', 'SARS-CoV2 N', 'SARS-CoV2 ORF10']

Read the Immune System graph

os.chdir('Immune_System')

netObj = ncip()
netObj.load_graph("Immune_System-medium-PPI.gml")

node_list = netObj.G_d.nodes.data()

ref_genes = [x[0] for x in node_list if x[1]['sequenced']!=0]

print(len(ref_genes))

1131

Identify graph nodes that match with the protein-protein interaction data.

CoV2_immune_interactions_node_id = {}

print('Directly interacting reference gene products:\n')

for CoV2_protein in SARS_CoV2_pnames:
    CoV2_immune_interactions_node_id[CoV2_protein] = []

    CoV2_immune_interactions_node_id[CoV2_protein] = [hp for hp in CoV2_interactions[CoV2_protein] if hp in ref_genes and hp not in CoV2_immune_interactions_node_id[CoV2_protein]]

    if len(CoV2_immune_interactions_node_id[CoV2_protein])==0:
        del CoV2_immune_interactions_node_id[CoV2_protein]
    else:
        print(CoV2_protein,CoV2_immune_interactions_node_id[CoV2_protein])

all_interacting_nodes = []
for v in CoV2_immune_interactions_node_id.values():
    all_interacting_nodes += v

Directly interacting reference gene products:

SARS-CoV2 Nsp2 ['EIF4E2']
SARS-CoV2 Nsp7 ['CYB5R3', 'RALA']
SARS-CoV2 Nsp8 ['HECTD1']
SARS-CoV2 Nsp12 ['RIPK1']
SARS-CoV2 Nsp13 ['TBK1']
SARS-CoV2 Nsp14 ['IMPDH2']
SARS-CoV2 Nsp15 ['RNF41']
SARS-CoV2 ORF3a ['HMOX1']
SARS-CoV2 M ['STOM']
SARS-CoV2 ORF8 ['ITGB1', 'PVR', 'IL17RA', 'NEU1']
SARS-CoV2 ORF9b ['TOMM70']
SARS-CoV2 ORF9c ['NLRX1', 'ECSIT']
SARS-CoV2 ORF10 ['ELOC', 'ELOB']

pathway_nametag = 'Immune_System'

json = json.dumps(CoV2_immune_interactions_node_id)

f = open('SARS_CoV2-'+pathway_nametag+'_interactions.json','w')

f.write(json)

f.close()

Set direct interaction with SARS-CoV-2 as a ‘True’ or ‘False’ attribute of the network node and save it to the NetworkX graph

SARS_nodes = {}

for n in netObj.G_d.nodes:
    check = False
    for CoV2_protein in CoV2_immune_interactions_node_id.keys():
        if n in CoV2_immune_interactions_node_id[CoV2_protein]:
            check = True

    SARS_nodes[n] = check

network_type = 'medium-PPI'

G_d = nx.read_gml(pathway_nametag+"-"+network_type+".gml")

nx.set_node_attributes(G_d, SARS_nodes, "covid")

nx.write_gml(G_d,pathway_nametag+"-"+network_type+".gml")

node_class = nx.get_node_attributes(G_d,"class")
node_covid = nx.get_node_attributes(G_d,"covid")

node_schemaClass = {}

for n in G_d.nodes:
    if node_covid[n]==True:
        node_schemaClass[n] = "SARSCoV2"
    else:
        node_schemaClass[n] = node_class[n]

nx.set_node_attributes(G_d, node_schemaClass, "class")

nx.write_gml(G_d,pathway_nametag+"-"+network_type+"-plot.gml")