Dear all, I am working on the interaction network between lncRNA, miRNA and mRNA and I am confusing with two questions, would be greatly appreciated if your all could help me a little: 1. On the build network. I used several databases to identify the interaction/target between LncRNA with miRNA and miRNA with mRNA. The question is shall I select the overlapping of these interactions from different databases (validated one database with another one) or combine/merge these interactions from different dataset (from different algorithms). 2. On the selection ceRNA network, I noticed many methods is to select ceRNA network with topological methods. I really did not understand the association between these topological with the biological function. could some one give me a little advice? Thanks and with best regards, Micheal
It all depends on the biological interpretation of the network. If your network is not so big, you may want to include all the interactions. On the other hand, if the network is too big, you may wish only to consider overlapping interactions. Sometimes you can also use the threshold based on interactions found in these many numbers of minimum databases.
thanks for the response! The questions is that if I include all the interactions, the network it too big about 5k interactions. If I use the overlapping, there are only 200 hundreds interactions.