Network Biology is fairly new to me so any suggestions or recommended software suggestions would be very much appreciated.
@Jochen: Thank you for your comment. To add to this question, I was able to determine all affected biochemical networks (oxidative stress, ER stress, NADPH pathways, calcium signaling, caspases, cell death signaling) only through experimentation (ELISA, colorimetric, and fluorometric assays).
Most of the networks I studied are interconnected (ER and oxidative stresess; calcium and ER sress; calcium and caspases; oxidative stress and cell death; oxidative stress and calcium etc.) which made things more confusing.
To further add to my query, how do I give a proper mathematical/quantitative definition of my variable? Also, in this case, is the variable the toxin?
@Jochen: I think I get what you want to say. It actually does make sense. I already have the data, so its up to me to find/measure "how much" is affected in the network. Having establish which network is affected and by "how much" then I think I can postulate on which network is the most affected or favored. Makes complete sense to me. Thank you so much for the advise...or the pull to the right direction ;)
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