how to extract genes from GO category from a non model organism

Question

[upendrakumar.devisetty]

Hi, i have done GO enrichment using GO-Seq on my RNA-Seq experiment and generated table that looks like this..

category       over_represented_pvalue     under_represented_pvalue     numDEInCat     numInCat     term                                  ont
GO:0030198     1.19E-07                    0.999999975                  21             153          extracellular matrix organization     BP
GO:0009612     9.85E-07                    0.999999904                  10             40           response to mechanical stimulus       BP
GO:0022617     1.40E-05                    0.999998078                  10             52           extracellular matrix disassembly      BP

What if I wanted to know what DE genes falls under a particular GO category (eg. "GO:0030198"). How do I do that? I am working on a non-model organism (Brassica rapa).

Thanks
Upendra

[Renesh]

Where is the DE genes column in this table? Please post complete table.

[upendrakumar.devisetty]

Why would there be a DE genes column in GO enrichment table after GO-Seq? I don't think so..

Answer 1

[Renesh]

Some GO analysis tools provides the genes corresponding to particular category. In this case, you dont have DEG column. If you want to know what DEG it corresponds to particular GO category, you need to protein blast (blastx) your DEG nucleotide sequences with UniProt database and fetch GO IDs from there. For this you can use Blast2Go tool.