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I am working on network analysis of differentially expressed genes, but the problem I am facing is that the gene set is very small (around 16 genes only), so when I'm trying to build an interaction network with these genes using STRING, the nodes starts to dissociate from the interaction when I set the confidence score to 0.400 or above (as the genes are related to Homo sapiens).

DE gene network has to be made in cytoscape, for that STRING ppi interactions are needed, that interaction network will tell us co-expression, homology etc and provide us a combined score.

So, to build an interaction network between these genes, I have to decrease the confidence score to 0.150 since it is only with this score that I am finding interactors.

So, I want to ask whether this low confidence score is valid for this short gene set related to Homo sapiens or, if not, what should I do in this case?

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  • $\begingroup$ Why do you think there should be a connection between these genes or proteins? Are you working with genes and trying to build a gene regulatory network or are you working with proteins and trying to build a protein-protein interaction network? $\endgroup$
    – terdon
    Jun 8 at 11:03
  • $\begingroup$ We really can't help unless you explain why you think there should be connections between these genes and why that connection would be detectable from PPI networks as opposed to gene regulatory networks. $\endgroup$
    – terdon
    Jun 11 at 13:36

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