How to find target genes From RNA seq data?

Question

[Fizzah]

Hello,

I am working on Differential Gene Expression analysis of 2 different cotton varieties. After finding DEGs from RNA seq data the next step is annotation and I need help in that

I am trying to find genes that are involved in somatic embryogenesis of cotton. I have performed Go ontology and found Top biological, molecular and cellular processes based on number of DEGs but now I don't know how to select my target genes now

Please guide

How I will I selectively analyze my target genes (which are responsible for somatic embryogenesis)

[Ram]

I don't know how to select my target genes now

Your target depends on ... you know, your goal. What biological question are you trying to answer? We cannot help you find purpose, we can help you if you stumble on your way to getting to a goal.

[Fizzah]

Yes I know but what I need to know is

Do I need to search selected biological cellular and molecular process to know which one is involve in somatic embryogenesis and then identify genes (probably via KEGG)

OR should I need to search all the reported genes in literature related to my hypothesis and then use them as a filter to find out target genes??? But in that case how will I get to know novel genes????

I hope you can get my point now

[Ram]

You've already identified GO terms, so why not go that route completely? That way, you'll at least let the data lead you where it does. Ideally, you have a hypothesis but not an agenda and your results will either support your hypothesis or not. Your DEGs might not pertain to somatic embryogenesis, but that's still a valid result. I don't understand why you have a set of target genes already but not a target pathway/biological mechanism.