Profiling differentially expressed genes

[Parharn]

Hi,
I am new to RNA-seq field. I managed to successfully find differentially expressed genes between to conditions. They are like couple of thousands. I am sure there are softwares out there that categorize and find the relations between them rather than looking them up one by one myself. So how do you approach it? Which softwares do you recommend?

Thanks,
Parham

[DonDolowy]

Tjenar tjenar,

you could either run GSEA on the dataset to see what gene sets are enriched in your conditions or you could go for GO analysis on your differentially expressed genes.

[Parharn]

Tjenare,
Danke schön. I will try GSEA. Is there any other software you know of?

[DonDolowy]

Yep, check out http://www.broadinstitute.org/gsea/