protein-protein interaction network
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
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Kevin Blighe
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zelda •
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zelda •
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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
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Have you tried downloading STRING? It is easy to create a network by parsing for protein pairs that are in your list.
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)?