how to make a graph from CoIP

Question

[Learner]

I am wondering if anyone can guide me toward this. we try to pull down a protein fo interest and we get what proteins come with it assuming that they belong to a complex. We have an abundance for each protein. lets say 100 proteins and 100 abundance. is there any way that I can make a network between these guys based on their abundance? I would appreciate any comment

Answer 1

[Jean-Karim Heriche]

A graph is a set of edges connecting nodes. In this case, the nodes would be the proteins. You can put an edge between proteins found to co-immunoprecipitate in two ways: - in the spoke model, you put an edge only between the bait (i.e. the protein you pulled down) and the preys (i.e. the proteins you identified as interactors of the bait) - in the matrix model, you put an edge between any pair of proteins (i.e. also between the preys) Now, you can try to use the abundance values to weight the edges. How you do it depends on what you want this weight to represent and what your abundance values are. A possible weighting scheme could be the product of relative abundances which can be loosely interpreted as a probability of interaction.

[Learner]

@Jean-Karim Heriche can you please give me a small example? I can try to make it . I believe product would be great