I am looking for both a didactic or simply a useful out-of-workbench tool that one can use to predict or play around modifying key factors in, say, receptor tyrosine kinase metabolic signaling pathways? I know many of these pathways are both cell type- and stimulus-dependent, but it would be useful to have these pathways not just as webmaps of interactomes you see in reviews or industry websites, but also as interactive webs that one can take or perhaps even give to students to play with, and thus better understand the functional relationship between different pathways/proteins. For example, I would like to determine the effect that upregulating Foxo genes, or PKCs, or inhibiting Ras or mTOR would have on migration, or proliferation or lipogenesis? Currently I am playing with just looking at reviews and mapping various interaction nodes and thought-experimenting on changes, but computer-modeling this would be a lot more productive, faster and easier. Anyway, if you know of such website or endeavor or have any thoughts/comments, please let me know. Thanks.
Dear Alfredo,
unfortunately I am not aware of such a tool, but there were attempts starting long ago in the PKA field by Buxbaum and Dudai (J Biol Chem. 1989 Jun 5;264(16):9344-51.
A quantitative model for the kinetics of cAMP-dependent protein kinase (type II) activity. Long-term activation of the kinase and its possible relevance to learning and memory.) I think it would be a nice collaborative project for a mathematician/programmer and a biologist/biochemist/pharmacologist and I would be very interested if something like this already exists or is in progress!!
Here are a few more papers that have been figuring out the workflow and the math
http://www.jbc.org/content/278/47/46506.full
http://www.hindawi.com/journals/cmmm/2014/340758/
http://rsif.royalsocietypublishing.org/content/3/9/515.long#
http://www.jbc.org/content/278/9/7278.full
it would be interesting to integrate these formulas and maps into something resembling a Boltzmann Machine using an environment like R.
http://www.r-bloggers.com/restricted-boltzmann-machines-in-r/
Dear Yuri,
thanks for the interesting links! I hope I understand at least a bit what has been done...
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