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I have not found any work which investigates assessment of differences in levels of secreted proteins by taking advantage of differential expression of the genes which mediate the secretory pathway.
For example, suppose the gene whose product binds specifically to a certain signal peptide is down-regulated. I would assume that this implies a down-regulation in all the levels of secreted proteins to which it binds.
Is such an analysis possible to date? If so, where?
Thanks in advance.
This is something that Qiagen's Ingenuity Pathway Analysis is meant to solve. Unfortunately, the process of solving pathway dependency problems like these is difficult, and frequently leads to the discovery of super-linked proteins that are seen everywhere (and consequently fairly uninteresting from a biological perspective). The challenge is in filtering out the useless noise of "statistical significance", and identifying the biologically-significant signal. That's not something that computers are particularly good at doing at the moment.
My own suggestion is that you would be better off finding someone who has domain knowledge in the area of secreted proteins, and trying to present results to them in such a way that it makes it easy to interpret the results and ask further questions. If you are that person, perhaps there's a more specific question that you could ask to further investigate the problem that you have.
