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Gene Ontonology analysis of DEGs from rice genome

Hello problem solver!

Your message is already clear, but I've made a few adjustments for grammar and flow:

I have obtained some DEGs from a single-cell transcriptomic analysis of rice samples. Currently, I am trying to perform gene ontology using bioMart goseq in R.

However, I am facing challenges while introducing R to the rice dataset and genome from EnsemblPlants. I cannot find a library for rice genome annotation to connect in R. For instance, there is a library available for the human genome - org.Hs.eg.db - but not for rice!

Could you please assist me in finding the rice (Oryza sativa japonica group) genome annotation link to connect in R? This would enable R to access information about gene IDs and gene/transcript lengths of my DEGs from the rice genome and, ultimately, provide me with GO annotation.

I have been working on this task for quite some time, and I even dedicated this weekend to the GO analysis! Now, I am eager to complete it as soon as possible!!!

Your valuable comments are truly appreciated!

Best,
Sadia Prity
First year Ph.D. study

gene-ontology rice genome-annotation
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written by prity6459 • prity6459

I don't see anything in Bioconductor like an org.db for rice other than MeSH.Osa.eg.db which appears to be deprecated. I think you'll have to provide gene id to GO term mappings by compiling that data from a different source. Have you tried biomaRt to pull GO accessions connected to your gene ids?

• 0 views • link
written by jv jv

Thank you so much for your response. Actually I dont find any sources for rice annotation to use in R. I will try biomaRt for GO accessions as you suggested. Thanks again! :)

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written by prity6459 • prity6459

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