So I have thought question I have been tacking for some time:
"You observe a known metabolite increasing in response to stress in a metabolomics experiment, how could you use transcriptomics and proteomics to determine whether the response is likely to be an impact of the stress or a defense mechanism?"
I am not sure if my answer is correct but I have a vague idea about how to answer this and I am looking for some feedback/improvements on it:
I believe that with transcriptomics we can determine the levels of mRNA in the system which we then could use to compare with our metabolic data and see if there is any correlation with the two. For instance if we do find a correlation (the accumulation of mRNA leading to an accumulation of metabolites) then we can assume a defence response is taking place.
However, to ensure that the mRNA is being translated and is indeed what is causing the increase in metabolites, we can use proteomics to find the proteins expressed by the genome. So, if we find that the accumulation of a given mRNA results in the accumulation of its relevant protein (eg: a catalytic enzyme) and that in turn induces the accumulation of our metabolite, we can be relatively certain a defence response is taking place.
Is the above explanation a valid one? Having not worked with raw data before I am not sure what the differences in expression would be for a defence response vs stress impact. I sort of assumed a stress impact expression would have high metabolite levels/profile regardless of mRNA levels as the former is characterised by a high turnover rate.
Anyway, any suggestions, corrections, guidence etc would be much appreciated. Thanks
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Stress response and 'omics
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