2.8 years ago by
There are few things which you can do, but keeping in mind as Ram said is to dig a bit more into the literature of Arabidopsis sp where you can find publications having heat treatment vs control.
So there are many ways to do it:
1) Perform differential expression and find the top 150 DEGs (assess the significance of those DESs in terms of enrichment)
2) Take from literature of such heat treatment publications for your desired strain and try to see how many of the genes that you have found as DEGs overlap with the DEGs of the publication. If there is a significant amount of hit try to make a hypergeometric estimation of it and see if that overlap is significant or not. Asses the fold change of those hits. Fish out the pathways they are involved and see if these are important pathways or not and then select those genes that come from the top pathways and have recurrent hits in first few top pathways from your overlap list (this might be too stringent but still if you come out with a panel of 20-30 genes might be worth doing
3) Alternatively you can do pathway analysis for total DEGs and find the top significant pathways and check them in line with the publications to see if these are recurrent pathways or not. If so try to find the enrichment of your DEGs in those pathways to find top scoring enriched genes and you can in fact validate those genes
4) I do not usually prefer much GO categories but still you can try. For Biological process and Molecular functions, you can take the top GO terms and see to what over-representations they fall, and see if such terms are reported in your species literature or not for heat treatment designs. If you again try to find enrichment of your DEGs and perform qPCR for the top genes with high enrichment score and significance.
These should work out but then again no estimate of genes can be made directly. You have to find in the literature which are the most frequented GO terms or pathways involved for such work and the genes that concede such and try to see how your DEGs behave among them.