how to make a network of known cluster of proteins
I came across to make a plot of a bunch of proteins which experimentally found to make a cluster. Lets say I have 3 clusters. Each cluster consists of a number of proteins. How can I plot all the clusters together ? (not interacting with each other but just linked through centre or something like this ?
Cluster 1: Q9Y4Y9, P62310, Q9Y4Z0, Q9Y333 ,P62312, O15116
Cluster 2: Q9Y4Y9, P62310, Q9Y4Z0, Q9Y333, O95777, P62312
Cluster 3: O14497, P51532, Q8TAQ2, Q92922, P60709, O96019
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Do you want to link the clusters if they share proteins or do you want to link them arbitrarily ?
@Jean-Karim Heriche I don't want to share them based on their similar proteins , probably arbitrarily is the option. however sometimes they do share proteins, which makes me wonder that it would make sense to also link them through that. But then I ask myself what will happen to those clusters which have nothing in common to share with others ???
There are plenty of other ways of linking your clusters. It all depends on what you're trying to do/show. For example, you could link your clusters based on shared GO terms or any other attribute they can have. You could also have links of different types (this is called a multigraph).
@Jean-Karim Heriche would it be possible to give an example of first one ?