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I'm trying to determine whether certain organic chemicals will upregulate classes of proteins that possess deacylase activity. 

How would I go about this experiment? I'm assuming I would use some sort of assay but I'm not exactly sure how I'd go about it.

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One way of examining this is by looking at the transcriptome as a whole before and after the introduction of the chemical. I would use microarray or next generation sequencing RNA-seq technology to look on the expression level of all the genes after the introduction of the chemical, some inert control and no treatment control.

Then, you can calculate the relative fold change in expression of all genes, under treatment vs. control. Next, you can do a GO term enrichment of the significantly upregulated genes, and see if the term "deacylases" shows significant enrichment in genes that are upregulated under treatment vs. control.

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