how to extract genes from GO category from a non model organism
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
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upendrakumar.devisetty
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1 answer
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.
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Where is the DE genes column in this table? Please post complete table.
Why would there be a DE genes column in GO enrichment table after GO-Seq? I don't think so..