DyNet on metabolic network

Question

[Lin]

Hi, everyone, Have you ever tried to introduce DyNet to create an overlay of two metabolite networks? I worked on metabolism data and was trying to figure out the metabolite in net1 whose edges changed the most in net2. The EDGEs here were filtered by the significance of correlations between each two metabolites. I am confused about whether this step was right since it was not the same as the gene network. I can't find any article employing DyNet on metabolite networks. Do you have any ideas or suggestions?

Answer 1

[Scooter]

Greetings,

I haven't used DyNet, so I'm just guessing here. The typical use (according to the app page) would be to look for rewiring -- that is the presence or absence of shared edges between two nodes. I seems like that would work in your case, but I'm really not sure. Since you are using a correlation network, the interpretation of the results would certainly be different, but the algorithm should still work.

-- scooter

[Lin]

Thx for your advice. Yes, I was going to rank the rewiring score in my paper, to see the changes in correlation network. I am just not quite sure about the way I built up my Net1 and Net2. Is there any difference between filtering the EDGEs by the significance or by the r(correlation coefficient)? Or there is no such difference, just depending on the situation and the expected results?