Generating Interaction map

Question

[Adrian Pelin]

I want to bridge 2 protein interaction networks from 2 different papers.

The first dataset consists of protein-protein interactions in the human genome in the format:

Bait_A - Pray_1
Bait_A - Pray_2
Bait_A - Pray_3
Bait_B - Pray_1
Bait_B - Pray_4

The second dataset consist of viral proteins which have been shown to interact with the Prays of the first dataset, but not the Bait. So integrating them together we get:

Bait_A - Pray_1 (vProt_1, vProt_2)
Bait_A - Pray_2 (vProt_4)
Bait_A - Pray_3  (vProt_4)
Bait_B - Pray_1 (vProt_1, vProt_2)
Bait_B - Pray_4  (vProt_1, vProt_3)

Because one of these papers is fairly recent (PMID 30833792), I am not sure these are present in any databases.

What are some ways I could represent this, either in R or Cytoscape?

Answer 1

[Jean-Karim Heriche]

I would view this as a bipartite graph. Just construct it as you would any graph, e.g. from an edge list.
Unless you want to use a specific data set for the human protein-protein interactions, I would suggest to use aggregated interaction data from e.g. STRING or iRefIndex. The representation you choose also depends on what you want to do with it.

[Adrian Pelin]

Haven't considered that, will give it a shot thanks!