protein-protein interaction network

Question

[zelda]

Hi,

I need to construct a protein-protein interaction network using a large gene list. I have tried STRING but the number of genes exceeded the limit (my gene list is around 4000). Any suggestions for another simple tool?

Thanks in advance

[Mensur Dlakic]

Have you tried downloading STRING? It is easy to create a network by parsing for protein pairs that are in your list.

[zelda]

Thank you for your quick reply.

I have downloaded STRING and looked for examples to use in R but since I am new to R, I couldn't find what I am looking for. Do you know how can I use STRING in R to create a protein-protein interaction network (Homo sapiens)?

Answer 1

[Kevin Blighe]

Hi Zelda,

You could try igraph (R) or Cytoscape. WGCNA (R) should be a consideration, too.

For igraph, I have a tutorial: Network plot from expression data in R using igraph

Kevin

[zelda]

Thank you so much!!