The best way to get the biologically meaningful interpretation from differentially expressed genes (DEG)

Question

[seta]

Hi all friends,

I have done a de novo transcriptome assembly of a non-model plant (no reference genome is available) and some analysis to get differentially expressed genes (DEG) with different packages, but I don't know which analysis lead me to more biologically meaningful DEG gene list. I was wondering how we can obtain the biologically meaningful interpretation from DEG? One answer may be GO analysis, but the output of this analysis is general, not specific and not much helpful at least for a non-model organism, like my case. Please let me know your experience on this issue.

Thank you

[cbio]

Give Enrichr a try for GO Analysis, it's not as 'broad' as other tools so it might be helpful. Also you might want to give something like motif analysis a shot?

I haven't spent much time working with RNA-seq data, so that's all I can really recommend at the moment. But at least until someone more experienced comes along to help out.

[seta]

It sounds that Enrichr cover human not plants. Actually, I want to compare different analysis to get differentially expressed genes and know which one gave me more biologically meaningful DEG gene list.