What’s the Answer? (PPI images in compartments)

BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question is another one of my favorite types–looking for better visualization tools to represent some data features. This time it’s protein-protein interactions (PPI), but organized on the graphical view to show different locations where they are occurring. Maybe it’s nuclear and cytoplasm, maybe it’s Golgi, maybe mitochondria, etc. I’ve seen some graphics like this and I get the utility. And IPA (we assume is the Ingenuity software) can do this it seems–but not everyone will have access to that. An open-source option would be great. But I haven’t tried to make them myself so I was interested to see the suggestions.


I am able to create decent PPI network pictures with cytoscape. But I recently noticed that IPA can produce nice visual of networks with membranes, cytoplasm, nucleus i.e. it shows different cellular location of proteins as well as interaction between them. But is there any free software that can produce nice visual of PPI along with such cellular components?

I would also like to know which free software do you use to create stunning visuals of networks.

Any comments will be greatly helpful.

Thanks Diwan

Go have a look at the suggestions. But if you know of some others that would be great too, do share.