Question: Adding more nodes to a PPI network?
gravatar for mendonca_thiago22
15 months ago by
mendonca_thiago220 wrote:

Hi everyone. I had to add more nodes to a Protein-Protein Interaction (STRING) network in order to get a better p value, but I'm not sure whether I should make assumptions on it since the main module and hub proteins derived from it are from the white nodes added (and not from my original gene list). What would you do? Discard the network and say that your list of genes did not generate a network or would you use the network with white nodes?

cytoscape ppi string network nodes • 304 views
ADD COMMENTlink modified 15 months ago by scooter380 • written 15 months ago by mendonca_thiago220
gravatar for scooter
15 months ago by
scooter380 wrote:

Well, the honest, but somewhat unhelpful, answer is "it depends". What is your p-Value based on? Are you doing some kind of GO enrichment? Where did your initial gene list come from? It's certainly possible that there are key proteins in pathways that aren't captured by typical transcriptomics or proteomics experiments, particularly if you are looking at fold changes. In that case, I would say that you should document what you did to add the extra proteins, note in particular the edge scores of those proteins and your gene list, and look for biological relevance of the additional proteins.

-- scooter

ADD COMMENTlink written 15 months ago by scooter380
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