Question: protein-protein interaction network
0
gravatar for zelda
5 months ago by
zelda20
zelda20 wrote:

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

ppi-network string • 184 views
ADD COMMENTlink modified 5 months ago by Kevin Blighe66k • written 5 months ago by zelda20
1

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

ADD REPLYlink written 5 months ago by Mensur Dlakic6.9k

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)?

ADD REPLYlink written 5 months ago by zelda20
1
gravatar for Kevin Blighe
5 months ago by
Kevin Blighe66k
Kevin Blighe66k wrote:

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

ADD COMMENTlink modified 5 months ago • written 5 months ago by Kevin Blighe66k
1

Thank you so much!!

ADD REPLYlink written 5 months ago by zelda20
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