What are the standard ways to visualize protein-protein or gene-gene interactions? I would like to visualize this interaction list.  Is there an online/web based way to do it? Is there a way to analyze the data?

Assuming I have exported the list into lines such as:

2  A2M 348 APOE
since I am not yet allowed to comment, I will have to pots this as an answer.

I guess Cytoscape (http://cytoscape.org/) would be a nice way to analyse such interaction lists/networks (still depends a bit on what you plan to do).

However, for this you will have to preprocess the downloadable excel sheet a bit.


save as tab-separated file (tsv)
run the below python3 script to format into an easily importable format for cytoscape. You can run the script as python3 script.py &lt;path-to-tsv-file&gt; &lt;delimeter for cytoscape&gt; . The new format is written to std out on the console, therefore maybe you need to write the output to a new file. A sample call could look like python3 testbench.py human_interactome_2017-06-12.tsv.csv ";". Make sure to add the delimeter in quotes.
you can then import the new file into cytoscape (import network as table) where the first column is your source, the third column your target and the middle column your interaction type.
Within cytoscape you can then adapt your edge style to vary the line type in a discrete mapping depending on the value of the interaction.


Screenshot from cytoscape:


Code below:

import sys

HIIIidx = 4
HII5idx = 5
venkatesanidx = 6
yuidx = 7
Litidx = 8

print(sys.argv)

if len(sys.argv) &lt;= 1:
    print("Usage: script.py file delimeter")

delim = ';'
inFile = sys.argv[1]

if len(sys.argv) &gt; 2:
    delim = sys.argv[2]


def printInteraction(syma, symb, inter):
    print(syma + delim + inter + delim + symb)


with open( inFile , 'r') as file:

    file.readline()

    for line in file:

        aline = line.strip('\n').split('\t')

        if aline[HIIIidx] == '1':
            printInteraction(aline[1], aline[3], 'HIII')

        if aline[HII5idx] == '1':
            printInteraction(aline[1], aline[3], 'HII5')

        if aline[venkatesanidx] == '1':
            printInteraction(aline[1], aline[3], 'VEN')

        if aline[yuidx] == '1':
            printInteraction(aline[1], aline[3], 'YU')

        if aline[Litidx] == '1':
            printInteraction(aline[1], aline[3], 'LIT')