what is the possibility of performing gene enrichment analysis when only one sample RNA-seq data is available. This is in hibernation study where no previous study exist on my organism. Can the data be compared to existing work in bear as an example. I am trying to see if certain genes that enable hibernation in bear can be found in my data and in what quantity. I read here that using up/down regulation is a misconception and should use gene enrichment. Thank you
Where did it say that using up/down regulation is a misconception? In your case, that would actually not be possible since you only have one group, so you might be misinterpreting that.
It says that it is misleading to use the term here A: What Does Up-Regulated And Down-Regulated Mean?. If I have one group, I guess I will not be able to determine the genes that maybe expressed. Someone suggested using GFOLD. Not sure of the possibility of doing the analysis that is why I am asking. Thank you for your response
As it says in that post:
I agree with that statement. However, they are questioning the proper term to use, not the general concept. In gene expression studies, you are comparing one group relative to another group. If you have one group, that is not possible.
I am assuming this the GFOLD you are referring to: https://www.ncbi.nlm.nih.gov/pubmed/22923299
Notice that GFOLD uses the distribution of fold changes. There is no fold change with only one group.