Adding human PPI to the network

This notebook identfies the proteins in the communication network built from Reactome and adds edges due protein-protein interactions (PPI). The human PPI data is taken from The Human Reference Protein Interactome Mapping Project.

import os, sys
import numpy as np
import scipy as sp
import pandas as pd
import copy as copy
from tqdm.notebook import tqdm
import math
import scipy.stats as st

from CoRe.ncip import ncip
from CoRe import reader

import matplotlib.pyplot as plt

import networkx as nx

Read protein-protein interaction data.

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

huPPI = pd.read_csv('ppi-genes.csv',header=None)

Read the nodes and the edges of the reactome information network.

selected_pathway = 'Immune System'
pathway_nametag = selected_pathway.replace(' ','_')

network_type = 'medium'

data_directory = "./" + pathway_nametag
os.chdir(data_directory)

edge_data = pd.read_pickle(pathway_nametag+'_'+network_type+'-edges.pkl')
node_data = pd.read_pickle(pathway_nametag+'_'+network_type+'-nodes.pkl')
all_nodes = node_data['node']

Identify the nodes in the network that have PPI, and add them as additional edges to the network.

c = 0

for i,row in tqdm(huPPI.iterrows()):
    hu1, hu2 = row[0], row[1]

    x = all_nodes[all_nodes == hu1]
    y = all_nodes[all_nodes == hu2]

    if len(x)>0 and len(y)>0:
        df_temp = pd.DataFrame([[hu1,hu2,'PPI','PPI','PPI','PPI']],columns=['input','output','reaction','name','schemaClass','module'])
        edge_data = pd.concat([edge_data,df_temp],sort=False,ignore_index=True)

        c += 1

print('Total protein-protein interactions to add:',c)

0it [00:00, ?it/s]

Total protein-protein interactions to add: 532

Create the communication network with the combined reactome and interactome edges.

netmaker = ncip()
netmaker.load_data(edge_data,node_data)

netmaker.save_edges_and_nodes(pathway_nametag,network_type)

netmaker.make_graph()
netmaker.save_network(pathway_nametag,network_type)

100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20813/20813 [00:01<00:00, 14931.90it/s]

Communication network Immune_System-medium.gml created.

Remove self-loops that are not regulatory reactions.

sl = list(nx.selfloop_edges(netmaker.G_d))

for e in sl:
    if 'regulation' not in netmaker.G_d[e[0]][e[1]]['category']:
        netmaker.G_d.remove_edge(e[0],e[1])

Remove isolates, or nodes that are note connected to any other node in the network.

ni = list(nx.isolates(netmaker.G_d))

for n in ni:
    netmaker.G_d.remove_node(n)

Save the network with the PPI edges.

netmaker.save_network(pathway_nametag,network_type+'-PPI')
netmaker.save_edges_and_nodes(pathway_nametag,network_type+'-PPI')

Communication network Immune_System-medium-PPI.gml created.