I have a question about "network score" of IPA Network analysis. In many papers, the top 5 networks were listed in tables, while in these tables some network scores are high (around 50), but others are low (less than 20). We use the same method for network analyses, and got the impression that we can see tight association between genes when "the network score" is higher than 40. However, we have not found literature discussing the meaningful "network score" (we found one paper described that “the networks are selected if their score is higher than 21”). We would appreciate it if you could let us know information about such a meaningful network score or your impression/experience of the network score (for example, did you see tight association of genes when the network score was less than 20?).
Last time I used IPA, the network score was just the number of genes in the network (including those in the your query gene list as well as those added through indirect interactions). There was no statistical test, and the scores will obviously vary with the number of genes in the gene lists (larger gene lists should produce larger networks).
Nevertheless, biologists often liked this function because some patterns come out when you visually inspect the networks (like maybe 80% of the genes in the network are connected to NFkB). In my opinion, I think the upstream regulator function provides a more rigourous way to identify regulatory hubs, but there point is that there are some people who like the network function (although I think it is important to realize that there is no statistical methodology behind that score)