hi i really need advise, kind of in a dilemma.
my RNA-seq data has shown about 430 DEGs based on cut off of 2 fold change, and p-value <0.05. That seems like a reasonable and adequate amount of DEGs to study on further but i am in a dilemma when it comes to presenting the GO or pathway analyses. None of the GO/pathway terms are significantly enriched based on Q value. I am trying to reduce fold change to 1.5 fold hoping more DEGs would get me higher chance of enrichment in GO/Pathway analyses so that remains to be seen.
In the event that none of these terms are enriched even upon lowering cutoff, what is the best approach to take in presenting the RNA-SEQ data? I cant even say that for example ''genes involved in metastasis process'' is signicantly enriched because i have some DEGs scattered across the terms in bits and pieces.
The only way i can think of presenting the data is to just put a table indicating all the DEGs and their fold change/P values, followed by a validation of some of the genes by RT-PCR. Any better ideas on the direction i should take from here?