differentially expressed gene (DEG) sets in a certain tissue/developmental stage of the brain

[Polpt]

Hi everybody,

please excuse me if this could be a stupid question for most of you.

However, I was wondering how to correctly interpret the results of the GENE2FUNC for the differentially expressed gene (DEG) sets enrichment analyses when the significance (red bar) is both in the down- and up-regulated direction.

Many thanks in advance.

[Kyoko Watanabe]

Hi,

I am sorry for my slow response.

If your gene sets are significantly enriched in both up and down DEGs, that means your genes are generally enriched in DEG of that tissues.

I split DEG into up and down so you can break down if your genes are specific to one direction.

You could say, your genes are specific to the tissue you are seeing the enrichment in both up and down DEGs.

This means when those genes are somehow affected, and if some of up DEGs are under-expressed or down DEGs are over-expressed, which can affect the function of the tissue.

This is just one way of understanding the results, of course, the enrichment test itself cannot prove it but I think the enrichment of DEG generally indicates tissue specificity of your genes.

Hope this helps.

Best,

Kyoko

[Junhao Wen]

HI, 

A follow-up question: 

How to interpret the DEG results: 

1. No significance in up-regulated DEG
2. No significance in down-regulated DEG
3. Sinigifincant in two-sided DEG.

Does this mean that my prioritized genes collectively overexpressed in both up-regulation and down-regulation? So we can not speculate that these genes somehow suppress or promote the gene transcription? Say this is related to producing a hormone at the protein level.