Hi guys, I have a question regarding the co-expression networks. In particular I have a gene marker and a list of co-expressed genes based on the mutual information. This list is around of 1000 genes (neighbourhood). Of course this is a not manageable number of genes. Is there a way to choose the best or representative number of genes-neighbors according to a threshold of MI value for example? I tried to rank the genes from the highly correlating to the lowly correlating but at some point I have to stop and choose a final number of genes. Is there a way to choose a cut-off point that could be "robust". I have no idea because I know that it depends on the final goal but in my case no experiments are feasible with this huge number of genes.
Could you help me please?
Thanks in advance