Hi,
I would be grateful for your opinion.
I performed a DGE analysis and received a list of differentially expressed genes.
Next, we focus on specific list of pre-defined genes for further analysis, since their biological functions are relevant for our scientific question (and all other differentially expressed genes will not be further included).
Since the list of genes-of-interest was selected by previous research I thought to run a functional enrichment analysis on those pre-defined genes to reassure that they are truly represent the biological functions we assume they are.
That is different from functional enrichment analyses I performed in the past, which were on all the differentially expressed genes.
Do you think our approach is reasonable?
thanks!
I think this approach is quite reasonable given that DEG analysis would produce rather broader GO annotation terms, for instance, 'covalent chromatin modification', however, using the genes listed in this particular term for functional enrichment would yield greater details about modifications e.g. methylation, acetylation etc on histones or nucleic acids.
Yes, the approach is reasonable. As you are narrowing down the analysis to pre-defined genes, as you are running functional enrichment analysis on these genes will serve as validation to strengthen the biological analysis of your DEGs. In addition to Vipul Batra I would suggest pathway analysis and network-based approaches to reveal key regulatory hubs, identify potential biomarkers, and elucidate complex biological mechanisms.
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