Question: how to extract genes from GO category from a non model organism
0
gravatar for upendrakumar.devisetty
5.7 years ago by
United States
upendrakumar.devisetty360 wrote:

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
GO:0010628 1.72E-05 0.999996653 13 90 positive regulation of gene expression 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

go non model • 2.6k views
ADD COMMENTlink modified 5.7 years ago by Renesh1.8k • written 5.7 years ago by upendrakumar.devisetty360

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

ADD REPLYlink written 5.7 years ago by Renesh1.8k
1

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

ADD REPLYlink written 5.7 years ago by upendrakumar.devisetty360
0
gravatar for Renesh
5.7 years ago by
Renesh1.8k
United States
Renesh1.8k wrote:

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.

ADD COMMENTlink written 5.7 years ago by Renesh1.8k
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