GO annotation for rice in an R package

Question

[djyjin]

Anyone that could give me an example for GO annotation of species Rice with an R package. My rice ID is like "LOC_Os01g01312". It's a location ID. Thanks.

[rohitsatyam102]

Hi @djyjin

Were you able to figure this out? I am experiencing a similar challenge

[prity6459]

Hi @djyjin and rohitsatyam102

I have also been facing challenges while conducting goseq analysis in R. I have obtained DEGs from rice samples, including gene ID, logFC, and adjusted p-value. I am using the script mentioned below. However, since this script requires the rice dataset (rg.Os.eg.db) and I cannot find this dataset in BiocManager or BiomaRt, I am unable to complete my analysis. :(

I was wondering if you have already found a way to perform the goseq analysis that you could share with me, please?

I hope this message finds you well. Have a nice day!

Sadia

[GenoMax]

Rice genome annotation project has moved to http://rice.uga.edu/. Since Rice used those project specific ID's your best bet may be to get the GO annotation from http://rice.uga.edu/annotation_pseudo_goslim.shtml

You can email the site maintainers to see if there is a way to download the GO terms for all rice proteins.

[prity6459]

Thanks a lot for your response!

You are correct that I can have GO terms from Rice genome annotation project and I already have them. Still I have been trying to get the GO pathways through goseq analysis since in most of the articles they mentioned using R packages instead of RAP-DB

That is why I was asking for the rice annotation packages to use in R. :,)

[Ron]

Check out this paper : http://nar.oxfordjournals.org/content/early/2013/04/29/nar.gkt281.full